SPEM1 (spermatid maturation 1) - Rat Genome Database

Name: SPEM1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: SPEM1 (spermatid maturation 1) Homo sapiens

Analyze

Symbol:

SPEM1

Name:

spermatid maturation 1

RGD ID:

1602954

HGNC Page

HGNC:32429

Description:

Predicted to be involved in flagellated sperm motility and sperm individualization. Predicted to act upstream of or within spermatogenesis. Predicted to be located in membrane. Predicted to be active in cytoplasm.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

C17orf83; chromosome 17 open reading frame 83; FLJ40081; spermatid maturation protein 1

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Mus musculus (house mouse):	Spem1 (spermatid maturation 1)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Spem1 (spermatid maturation 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Chinchilla lanigera (long-tailed chinchilla):	Spem1 (spermatid maturation 1)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	SPEM1 (spermatid maturation 1)	NCBI	Ortholog
Canis lupus familiaris (dog):	SPEM1 (spermatid maturation 1)	HGNC	HomoloGene, NCBI
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Spem1 (spermatid maturation 1)	NCBI	Ortholog
Chlorocebus sabaeus (green monkey):	SPEM1 (spermatid maturation 1)	NCBI	Ortholog
Heterocephalus glaber (naked mole-rat):	Spem1 (spermatid maturation 1)	NCBI	Ortholog
Other homologs ²
Rattus norvegicus (Norway rat):	Or52d3 (olfactory receptor family 52 subfamily D member 3)	HGNC	OMA
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Spem1 (spermatid maturation 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Spem1 (spermatid maturation 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	7,420,324 - 7,421,632 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	7,420,324 - 7,421,632 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	7,323,643 - 7,324,951 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	7,264,403 - 7,265,675 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	17	7,349,564 - 7,350,836 (+)	NCBI		Celera
Cytogenetic Map	17	p13.1	NCBI
HuRef	17	7,217,702 - 7,218,974 (+)	NCBI		HuRef
CHM1_1	17	7,332,771 - 7,334,043 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	17	7,324,372 - 7,325,680 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

common variable immunodeficiency (IAGP)

congenital myasthenic syndrome 2A (IAGP)

dyskeratosis congenita (IAGP)

genetic disease (IAGP)

intellectual disability (IAGP)

Li-Fraumeni syndrome (IAGP)

very long chain acyl-CoA dehydrogenase deficiency (IAGP)

Weissenbacher-Zweymuller syndrome (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

acrylamide (ISO)

benzo[a]pyrene (EXP)

bisphenol A (ISO)

C60 fullerene (ISO)

cadmium dichloride (EXP)

chlorpyrifos (ISO)

maleic acid (EXP)

resveratrol (EXP)

trichloroethene (ISO)

triptonide (ISO)

valproic acid (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell differentiation (IEA)

flagellated sperm motility (IBA,IEA,ISO)

sperm individualization (IBA,IEA,ISO)

spermatogenesis (IEA,ISO)

Cellular Component

cytoplasm (IBA,IEA)

membrane (IEA)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Abnormal esophagus physiology (IAGP)

Bilateral conductive hearing impairment (IAGP)

Intellectual disability, mild (IAGP)

Pierre-Robin sequence (IAGP)

References

References - curated

#	Reference Title	Reference Citation
1.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:14702039	PMID:17426145	PMID:20558241	PMID:21184802	PMID:21873635	PMID:26186194	PMID:28514442	PMID:30054974	PMID:33961781

Genomics

Comparative Map Data

SPEM1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	7,420,324 - 7,421,632 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	7,420,324 - 7,421,632 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	7,323,643 - 7,324,951 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	7,264,403 - 7,265,675 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	17	7,349,564 - 7,350,836 (+)	NCBI		Celera
Cytogenetic Map	17	p13.1	NCBI
HuRef	17	7,217,702 - 7,218,974 (+)	NCBI		HuRef
CHM1_1	17	7,332,771 - 7,334,043 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	17	7,324,372 - 7,325,680 (+)	NCBI		T2T-CHM13v2.0

Spem1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	69,711,697 - 69,712,991 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	69,711,702 - 69,713,006 (-)	Ensembl		GRCm39 Ensembl
GRCm38	11	69,820,871 - 69,822,165 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	69,820,876 - 69,822,180 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	69,634,373 - 69,635,667 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	69,637,066 - 69,638,375 (-)	NCBI		MGSCv36	mm8
Celera	11	77,381,831 - 77,383,125 (-)	NCBI		Celera
Cytogenetic Map	11	B3	NCBI
cM Map	11	42.89	NCBI

Spem1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	55,040,178 - 55,041,479 (-)	NCBI		GRCr8
mRatBN7.2	10	54,541,454 - 54,542,755 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	54,541,471 - 54,546,131 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	59,203,960 - 59,205,260 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	58,692,526 - 58,693,826 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	54,200,206 - 54,201,504 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	56,428,447 - 56,429,748 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	56,428,344 - 56,429,833 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	56,173,566 - 56,174,867 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	56,642,947 - 56,644,248 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	10	53,695,730 - 53,697,031 (-)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

Spem1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955467	9,503,229 - 9,504,535 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955467	9,503,229 - 9,504,535 (-)	NCBI	ChiLan1.0	ChiLan1.0

SPEM1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	19	15,017,267 - 15,018,936 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	17	16,983,062 - 16,984,394 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	7,454,453 - 7,455,791 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	7,441,032 - 7,442,342 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	7,441,032 - 7,442,342 (+)	Ensembl	panpan1.1		panPan2

SPEM1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	32,354,044 - 32,357,684 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	32,354,153 - 32,355,401 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	32,491,884 - 32,493,545 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	32,459,456 - 32,461,117 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	5	32,459,816 - 32,461,064 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	5	32,424,690 - 32,426,351 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	5	32,383,422 - 32,385,083 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	5	32,560,690 - 32,562,351 (+)	NCBI		UU_Cfam_GSD_1.0

Spem1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	47,230,596 - 47,232,168 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936595	705,138 - 706,328 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936595	704,717 - 706,357 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SPEM1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	16	6,796,398 - 6,798,093 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	6,796,842 - 6,798,058 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666059	14,610,480 - 14,612,166 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Spem1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624786	10,034,685 - 10,036,388 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624786	10,034,794 - 10,038,171 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in SPEM1
26 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 17p13.2-13.1(chr17:5732977-8038822)x1	copy number loss	See cases [RCV000051043]	Chr17:5732977..8038822 [GRCh38] Chr17:5636297..7942140 [GRCh37] Chr17:5577021..7882865 [NCBI36] Chr17:17p13.2-13.1	pathogenic
GRCh38/hg38 17p13.1(chr17:6958978-8335684)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052457]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052457]\|See cases [RCV000052457]	Chr17:6958978..8335684 [GRCh38] Chr17:6862297..8239002 [GRCh37] Chr17:6803021..8179727 [NCBI36] Chr17:17p13.1	pathogenic
GRCh38/hg38 17p13.2-13.1(chr17:6307904-8842949)x1	copy number loss	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053407]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053407]\|See cases [RCV000053407]	Chr17:6307904..8842949 [GRCh38] Chr17:6211224..8746266 [GRCh37] Chr17:6151948..8686991 [NCBI36] Chr17:17p13.2-13.1	pathogenic
GRCh38/hg38 17p13.1(chr17:7210345-7496934)x1	copy number loss	See cases [RCV000053425]	Chr17:7210345..7496934 [GRCh38] Chr17:7113664..7400253 [GRCh37] Chr17:7054388..7340977 [NCBI36] Chr17:17p13.1	pathogenic
NM_199339.2(SPEM1):c.839C>T (p.Ala280Val)	single nucleotide variant	Malignant melanoma [RCV000071688]	Chr17:7421514 [GRCh38] Chr17:7324833 [GRCh37] Chr17:7265557 [NCBI36] Chr17:17p13.1	not provided
GRCh38/hg38 17p13.1(chr17:6958978-7491129)x3	copy number gain	See cases [RCV000133763]	Chr17:6958978..7491129 [GRCh38] Chr17:6862297..7394448 [GRCh37] Chr17:6803021..7335172 [NCBI36] Chr17:17p13.1	uncertain significance
GRCh38/hg38 17p13.3-13.1(chr17:198748-7491129)x3	copy number gain	See cases [RCV000134970]	Chr17:198748..7491129 [GRCh38] Chr17:50690..7394448 [GRCh37] Chr17:48539..7335172 [NCBI36] Chr17:17p13.3-13.1	pathogenic
GRCh38/hg38 17p13.2-12(chr17:5732953-12095349)x3	copy number gain	See cases [RCV000134851]	Chr17:5732953..12095349 [GRCh38] Chr17:5636273..11998666 [GRCh37] Chr17:5576997..11939391 [NCBI36] Chr17:17p13.2-12	pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:162016-7697012)x1	copy number loss	See cases [RCV000138214]	Chr17:162016..7697012 [GRCh38] Chr17:45835..7600330 [GRCh37] Chr17:11807..7541055 [NCBI36] Chr17:17p13.3-13.1	pathogenic
GRCh38/hg38 17p13.2-13.1(chr17:6361393-7750863)x3	copy number gain	See cases [RCV000138220]	Chr17:6361393..7750863 [GRCh38] Chr17:6264713..7654181 [GRCh37] Chr17:6205437..7594906 [NCBI36] Chr17:17p13.2-13.1	likely pathogenic
GRCh38/hg38 17p13.3-12(chr17:162016-12343901)x3	copy number gain	See cases [RCV000138531]	Chr17:162016..12343901 [GRCh38] Chr17:45835..12247218 [GRCh37] Chr17:11807..12187943 [NCBI36] Chr17:17p13.3-12	pathogenic
GRCh38/hg38 17p13.3-12(chr17:150732-14764202)x3	copy number gain	See cases [RCV000142236]	Chr17:150732..14764202 [GRCh38] Chr17:525..14667519 [GRCh37] Chr17:525..14608244 [NCBI36] Chr17:17p13.3-12	pathogenic
GRCh37/hg19 17p13.1(chr17:7241916-8692213)x1	copy number loss	See cases [RCV000445992]	Chr17:7241916..8692213 [GRCh37] Chr17:17p13.1	pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)	copy number gain	See cases [RCV000511439]	Chr17:526..81041938 [GRCh37] Chr17:17p13.3-q25.3	pathogenic
GRCh37/hg19 17p13.3-12(chr17:525-15027737)x3	copy number gain	See cases [RCV000511786]	Chr17:525..15027737 [GRCh37] Chr17:17p13.3-12	pathogenic
GRCh37/hg19 17p13.1(chr17:6934163-8217978)x1	copy number loss	Poly (ADP-Ribose) polymerase inhibitor response [RCV000626431]	Chr17:6934163..8217978 [GRCh37] Chr17:17p13.1	drug response
NM_199339.3(SPEM1):c.719C>T (p.Ala240Val)	single nucleotide variant	Inborn genetic diseases [RCV003257037]	Chr17:7421394 [GRCh38] Chr17:7324713 [GRCh37] Chr17:17p13.1	uncertain significance
GRCh37/hg19 17p13.1(chr17:7094070-7414448)x1	copy number loss	See cases [RCV000512276]	Chr17:7094070..7414448 [GRCh37] Chr17:17p13.1	likely pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3	copy number gain	See cases [RCV000512441]	Chr17:526..81041938 [GRCh37] Chr17:17p13.3-q25.3	pathogenic
NC_000017.10:g.7124585_7400253dup	duplication	Robin sequence [RCV000677112]	Chr17:7124585..7400253 [GRCh37] Chr17:17p13.1	uncertain significance
Single allele	duplication	Isolated Pierre-Robin syndrome [RCV000677112]	Chr17:7124585..7400253 [GRCh37] Chr17:17p13.1	likely pathogenic
GRCh37/hg19 17p13.3-12(chr17:525-11186432)x3	copy number gain	not provided [RCV000683866]	Chr17:525..11186432 [GRCh37] Chr17:17p13.3-12	pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3	copy number gain	not provided [RCV000739320]	Chr17:7214..81058310 [GRCh37] Chr17:17p13.3-q25.3	pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3	copy number gain	not provided [RCV000739325]	Chr17:12344..81057996 [GRCh37] Chr17:17p13.3-q25.3	pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3	copy number gain	not provided [RCV000739324]	Chr17:8547..81060040 [GRCh37] Chr17:17p13.3-q25.3	pathogenic
GRCh37/hg19 17p13.1(chr17:7269373-7390669)x1	copy number loss	not provided [RCV000739395]	Chr17:7269373..7390669 [GRCh37] Chr17:17p13.1	benign
NM_199339.3(SPEM1):c.553G>A (p.Val185Ile)	single nucleotide variant	not provided [RCV000968338]	Chr17:7421228 [GRCh38] Chr17:7324547 [GRCh37] Chr17:17p13.1	benign
NC_000017.10:g.(?_6589506)_(8151374_?)dup	duplication	Common variable immunodeficiency [RCV001338841]\|Dyskeratosis congenita [RCV001031775]	Chr17:6589506..8151374 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.639C>G (p.Ser213Arg)	single nucleotide variant	Inborn genetic diseases [RCV003239657]	Chr17:7421314 [GRCh38] Chr17:7324633 [GRCh37] Chr17:17p13.1	uncertain significance
NC_000017.10:g.(?_7123304)_(7606804_?)del	deletion	Common variable immunodeficiency [RCV003107751]	Chr17:7123304..7606804 [GRCh37] Chr17:17p13.1	uncertain significance
GRCh37/hg19 17p13.1(chr17:6650649-8040151)x3	copy number gain	not provided [RCV001259299]	Chr17:6650649..8040151 [GRCh37] Chr17:17p13.1	pathogenic
NC_000017.10:g.(?_6328780)_(7606804_?)dup	duplication	Congenital myasthenic syndrome 2A [RCV003109217]\|Very long chain acyl-CoA dehydrogenase deficiency [RCV003119078]	Chr17:6328780..7606804 [GRCh37] Chr17:17p13.2-13.1	uncertain significance
GRCh37/hg19 17p13.1(chr17:7241916-8692213)	copy number loss	not specified [RCV002052586]	Chr17:7241916..8692213 [GRCh37] Chr17:17p13.1	pathogenic
GRCh37/hg19 17p13.1(chr17:7020054-8086290)	copy number loss	not specified [RCV002052585]	Chr17:7020054..8086290 [GRCh37] Chr17:17p13.1	pathogenic
NC_000017.10:g.(?_7120455)_(8151423_?)del	deletion	Li-Fraumeni syndrome [RCV003111420]	Chr17:7120455..8151423 [GRCh37] Chr17:17p13.1	pathogenic
NC_000017.10:g.(?_7123304)_(8193254_?)del	deletion	Very long chain acyl-CoA dehydrogenase deficiency [RCV003119081]	Chr17:7123304..8193254 [GRCh37] Chr17:17p13.1	pathogenic
NM_199339.3(SPEM1):c.764G>A (p.Arg255His)	single nucleotide variant	Inborn genetic diseases [RCV003279405]	Chr17:7421439 [GRCh38] Chr17:7324758 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.305T>C (p.Met102Thr)	single nucleotide variant	Inborn genetic diseases [RCV002688813]	Chr17:7420980 [GRCh38] Chr17:7324299 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.257A>G (p.Gln86Arg)	single nucleotide variant	Inborn genetic diseases [RCV002689125]	Chr17:7420932 [GRCh38] Chr17:7324251 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.359G>A (p.Arg120His)	single nucleotide variant	Inborn genetic diseases [RCV002863909]	Chr17:7421034 [GRCh38] Chr17:7324353 [GRCh37] Chr17:17p13.1	likely benign
NM_199339.3(SPEM1):c.663C>A (p.Asn221Lys)	single nucleotide variant	Inborn genetic diseases [RCV002883275]	Chr17:7421338 [GRCh38] Chr17:7324657 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.575C>T (p.Thr192Ile)	single nucleotide variant	Inborn genetic diseases [RCV002703935]	Chr17:7421250 [GRCh38] Chr17:7324569 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.911G>A (p.Arg304His)	single nucleotide variant	Inborn genetic diseases [RCV002782796]	Chr17:7421586 [GRCh38] Chr17:7324905 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.596G>C (p.Gly199Ala)	single nucleotide variant	Inborn genetic diseases [RCV002737380]	Chr17:7421271 [GRCh38] Chr17:7324590 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.643G>C (p.Glu215Gln)	single nucleotide variant	Inborn genetic diseases [RCV002767944]	Chr17:7421318 [GRCh38] Chr17:7324637 [GRCh37] Chr17:17p13.1	likely benign
NM_199339.3(SPEM1):c.314C>T (p.Ser105Phe)	single nucleotide variant	Inborn genetic diseases [RCV002743374]	Chr17:7420989 [GRCh38] Chr17:7324308 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.179T>C (p.Val60Ala)	single nucleotide variant	Inborn genetic diseases [RCV003004278]	Chr17:7420661 [GRCh38] Chr17:7323980 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.341G>A (p.Arg114His)	single nucleotide variant	Inborn genetic diseases [RCV002666441]	Chr17:7421016 [GRCh38] Chr17:7324335 [GRCh37] Chr17:17p13.1	likely benign
NM_199339.3(SPEM1):c.152G>T (p.Ser51Ile)	single nucleotide variant	Inborn genetic diseases [RCV002669495]	Chr17:7420634 [GRCh38] Chr17:7323953 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.101G>T (p.Gly34Val)	single nucleotide variant	Inborn genetic diseases [RCV002717478]	Chr17:7420485 [GRCh38] Chr17:7323804 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.340C>T (p.Arg114Cys)	single nucleotide variant	Inborn genetic diseases [RCV002963650]	Chr17:7421015 [GRCh38] Chr17:7324334 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.9G>C (p.Met3Ile)	single nucleotide variant	Inborn genetic diseases [RCV002939191]	Chr17:7420393 [GRCh38] Chr17:7323712 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.815G>A (p.Arg272Gln)	single nucleotide variant	Inborn genetic diseases [RCV002944956]	Chr17:7421490 [GRCh38] Chr17:7324809 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.898A>C (p.Asn300His)	single nucleotide variant	Inborn genetic diseases [RCV003201064]	Chr17:7421573 [GRCh38] Chr17:7324892 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.409C>T (p.Pro137Ser)	single nucleotide variant	Inborn genetic diseases [RCV003206064]	Chr17:7421084 [GRCh38] Chr17:7324403 [GRCh37] Chr17:17p13.1	uncertain significance
GRCh37/hg19 17p13.1(chr17:7004894-7766789)x1	copy number loss	not provided [RCV003222936]	Chr17:7004894..7766789 [GRCh37] Chr17:17p13.1	pathogenic
NM_199339.3(SPEM1):c.806G>C (p.Arg269Pro)	single nucleotide variant	Inborn genetic diseases [RCV003263571]	Chr17:7421481 [GRCh38] Chr17:7324800 [GRCh37] Chr17:17p13.1	uncertain significance
NM_199339.3(SPEM1):c.763C>T (p.Arg255Cys)	single nucleotide variant	Inborn genetic diseases [RCV003288576]	Chr17:7421438 [GRCh38] Chr17:7324757 [GRCh37] Chr17:17p13.1	uncertain significance
GRCh38/hg38 17p13.3-12(chr17:165730-11404096)x3	copy number gain	Chromosome 17p13.3 duplication syndrome [RCV003327726]	Chr17:165730..11404096 [GRCh38] Chr17:17p13.3-12	pathogenic
GRCh37/hg19 17p13.1(chr17:7002380-7469251)x1	copy number loss	not specified [RCV003987240]	Chr17:7002380..7469251 [GRCh37] Chr17:17p13.1	pathogenic
GRCh37/hg19 17p13.3-11.2(chr17:525-21510992)x3	copy number gain	not specified [RCV003987215]	Chr17:525..21510992 [GRCh37] Chr17:17p13.3-11.2	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	321
Count of miRNA genes:	289
Interacting mature miRNAs:	316
Transcripts:	ENST00000323675
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region

D17S1783

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	17	7,323,027 - 7,323,124	UniSTS	GRCh37
Build 36	17	7,263,751 - 7,263,848	RGD	NCBI36
Celera	17	7,348,912 - 7,349,009	RGD
Cytogenetic Map	17	p13.1	UniSTS
HuRef	17	7,217,050 - 7,217,147	UniSTS

RH15991

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	17	7,322,818 - 7,323,103	UniSTS	GRCh37
Build 36	17	7,263,542 - 7,263,827	RGD	NCBI36
Celera	17	7,348,703 - 7,348,988	RGD
Cytogenetic Map	17	p13.1	UniSTS
HuRef	17	7,216,841 - 7,217,126	UniSTS
GeneMap99-GB4 RH Map	17	53.39	UniSTS

A005P18

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	17	7,322,968 - 7,323,129	UniSTS	GRCh37
Build 36	17	7,263,692 - 7,263,853	RGD	NCBI36
Celera	17	7,348,853 - 7,349,014	RGD
Cytogenetic Map	17	p13.1	UniSTS
HuRef	17	7,216,991 - 7,217,152	UniSTS
GeneMap99-GB4 RH Map	17	46.58	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system

circulatory system

endocrine system

exocrine system

hemolymphoid system

hepatobiliary system

integumental system

musculoskeletal system

nervous system

renal system

reproductive system

respiratory system

sensory system

adipose tissue

appendage

High

Medium

359

Low

Below cutoff

947

1089

651

201

486

136

1978

870

1653

548

641

562

1281

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_199339	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC113189	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK097400	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC033882	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068261	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CS111500	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CS111510	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000323675 ⟹ ENSP00000315554

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	17	7,420,324 - 7,421,632 (+)	Ensembl

RefSeq Acc Id:

NM_199339 ⟹ NP_955371

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	17	7,420,324 - 7,421,632 (+)	NCBI
GRCh37	17	7,323,652 - 7,324,956 (+)	NCBI
Build 36	17	7,264,403 - 7,265,675 (+)	NCBI Archive
Celera	17	7,349,564 - 7,350,836 (+)	RGD
HuRef	17	7,217,702 - 7,218,974 (+)	RGD
CHM1_1	17	7,332,771 - 7,334,043 (+)	NCBI
T2T-CHM13v2.0	17	7,324,372 - 7,325,680 (+)	NCBI

Sequence:

show sequence

AGTGGACACTGTCGGCACGGTGGGCTGGGGGCGTAAGGGCCCCGGTGGTCCTAGGGACCCCATG
GCCATGGTTGAGCGGCCGAGGCCCGAGTGGGCCTCGTATCACAACTGCAACAGCAACAGCTGCC
AGGACCTGGGCAACTCTGTCCTGTTGCTGCTGGGCCTCATCATCTGCATTAACATTAGCATCAA
TATAGTGACCCTGCTCTGGAGCCGATTCCGTGGTGTCTTATACCAAGTGTTCCATGATACCATT
TGTGAGAAAGAAGCTCCCAAGTCATCATTACTCAGAAAGCAGACCCAGCCCCCTAAGAAGCAGA
GTTCTCCTGCAGTCCATCTTCGGTGCACCATGGACCCTGTGATGATGACTGTGTCCCCGCCCCC
AGCTCACCGCCATCGCCGTCGAGGCTCTCCCACACGCTGTGCTCACTGCCCAGTAGCTTGGGCT
CCTGACACTGATGACGAGAAGCCTCATCAGTACCCAGCCATCTGCTCCTACCACTGGGATGTCC
CTGAGGACTGGGAAGGCTTCCAACACACTCAGGGGACCTGGGTTCCCTGGTCTCAGGATGCCCC
AGAGTCCCCTCCCCAGACCATCCGCTTCCAGCCTACCGTAGAGGAAAGGCCCCTCAAAACAGGC
ATATGGTCCGAGCTGGGCCTAAGGGCCTATGTGTATCCTGTGAACCCCCCACCTCCCAGCCCTG
AGGCTCCTAGCCACAAGAACGGTGGGGAGGGGGCGGTGCCAGAGGCAGAGGCGGCTCAGTACCA
GCCTGTCCCAGCTCCCACCCTGGGCCCAGCAGTCATCCCTGAATTTTCCCGGCACCGCTCCTCA
GGCCGAATAGTGTATGATGCCCGGGACATGAGACGGCGGCTTCGGGAACTGACCCGGGAGGTGG
AGGCCCTGTCCGGCTGCTACCCCCTAGCCTCTGGATCCAGCACTGCCGAGGAGACAAGCAAGAA
TTGGGTGTACCGTTCCCTAACTGGGAGGTGACTGGAAAAAAATAAAAAGGAGAGAGGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_955371	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH33882	(Get FASTA)	NCBI Sequence Viewer
	BAC05034	(Get FASTA)	NCBI Sequence Viewer
	CAJ09938	(Get FASTA)	NCBI Sequence Viewer
	CAJ09939	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000315554
	ENSP00000315554.3
	ENSP00000492561.1
GenBank Protein	Q8N4L4	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_955371 ⟸ NM_199339

- UniProtKB:

Q8N4L4 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAMVERPRPEWASYHNCNSNSCQDLGNSVLLLLGLIICINISINIVTLLWSRFRGVLYQVFHDT
ICEKEAPKSSLLRKQTQPPKKQSSPAVHLRCTMDPVMMTVSPPPAHRHRRRGSPTRCAHCPVAW
APDTDDEKPHQYPAICSYHWDVPEDWEGFQHTQGTWVPWSQDAPESPPQTIRFQPTVEERPLKT
GIWSELGLRAYVYPVNPPPPSPEAPSHKNGGEGAVPEAEAAQYQPVPAPTLGPAVIPEFSRHRS
SGRIVYDARDMRRRLRELTREVEALSGCYPLASGSSTAEETSKNWVYRSLTGR

hide sequence

RefSeq Acc Id:

ENSP00000315554 ⟸ ENST00000323675

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q8N4L4-F1-model_v2	AlphaFold	Q8N4L4	1-309	view protein structure

Promoters

RGD ID:

7233741

Promoter ID:

EPDNEW_H22616

Type:

multiple initiation site

Name:

SPEM1_1

Description:

spermatid maturation 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	17	7,420,331 - 7,420,391	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:32429	AgrOrtholog
COSMIC	SPEM1	COSMIC
Ensembl Genes	ENSG00000181323	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSG00000284598	UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000323675	ENTREZGENE
	ENST00000323675.4	UniProtKB/Swiss-Prot
	ENST00000640564.2	UniProtKB/Swiss-Prot
GTEx	ENSG00000181323	GTEx
	ENSG00000284598	GTEx
HGNC ID	HGNC:32429	ENTREZGENE
Human Proteome Map	SPEM1	Human Proteome Map
InterPro	SPEM1_N	UniProtKB/Swiss-Prot
KEGG Report	hsa:374768	UniProtKB/Swiss-Prot
NCBI Gene	374768	ENTREZGENE
OMIM	615116	OMIM
PANTHER	SPERMATID MATURATION PROTEIN 1	UniProtKB/Swiss-Prot
	SPERMATID MATURATION PROTEIN 1	UniProtKB/Swiss-Prot
Pfam	Spem1	UniProtKB/Swiss-Prot
PharmGKB	PA162404476	PharmGKB
UniProt	Q8N4L4	ENTREZGENE, UniProtKB/Swiss-Prot

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Human Phenotype Annotations - ClinVar

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