RGD:11650507 Rat Genome Database

Variant: RGD:11650507 - Homo sapiens

RGD ID:

11650507

RS ID:

rs886054753

ClinVar ID:

CV282227

Genic Status:

GENIC

Type:

SNV (SO:0001483)

Associated Genes:

NPHP1

Reference Nucleotide:

Variant Nucleotide:

Position

Assembly	Chr	Position
GRCh37	2	110,904,403
GRCh38	2	110,146,826

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

ClinVar Data

HGVS Name(s)	Last Evaluated	Molecular Consequence	Clinical Significance	Age of Onset	Prevalence	Trait Synonyms
NG_008287.1:g.63237G>C NC_000002.12:g.110146826C>G NC_000002.11:g.110904403C>G NP_000263.2:p.Glu483Gln More...	01/13/2018	missense variant	uncertain significance	antenatal	1-9 / 100 000	Joubert syndrome 4; Joubert syndrome with renal anomalies; Juvenile nephronophthisis with Leber amaurosis; Nephronophthisis familial juvenile

Disease Annotations Click to see Annotation Detail View

Joubert syndrome 4 (IAGP)

nephronophthisis 1 (IAGP)

Senior-Loken syndrome (IAGP)

Senior-Loken Syndrome 1 (IAGP)

Variant Details

Variant Transcripts

Gene Symbol:	NPHP1
Accession:	XM_011511244
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	483

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQSRGRIFLVSKPVLQQINTVDV LTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMS IQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNS TGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQIMTMRRQPQLLVKLRSLNRR SRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKR SEKLSKPVSPREGKKKWPELYHILKTMHCSCLPCYKIMGLTSSSPKDPSTSIPGIAGNKPTTLDPMQNTCYNYLR*

Gene Symbol:	NPHP1
Accession:	NM_207181
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	482

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQSRGRIFLVSKPVLQINTVDVL TTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMSI QVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNST GQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQIMTMRRQPQLLVKLRSLNRRS RNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKRS EKRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQT YDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	XM_006712551
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	483

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQSRGRIFLVSKPVLQQINTVDV LTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMS IQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNS TGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQIMTMRRQPQLLVKLRSLNRR SRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKR SEKLSKPVSPREGKKKWPELYHILKTMHCSCLPCYKIMRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEETETARW KVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	XM_005263677
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	426

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRS RPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFI RSNSASPDLGILFELGISYIRNSTGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSV FYQIMTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPML LEQPDVMDALRSSWAGKESTLKRSEKLSKPVSPREGKKKWPELYHILKTMHCSCLPCYKIMRDKEFLKSTFLLVYHDCVL PLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	NM_001128179
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	364

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRVGAPTEEEEESESEDSEDSGGEEEDAEEEEEE KEENESHKWSTGEEYIAVGDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEE GSEEDVEAVDETADGAEVKQRTDPHWSAVQKAISEINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPS QLAFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTF SPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNSTGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPY EKGIEVDPSISRRAHGSVFYQIMTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMS LQSTDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEE TETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	XM_005263676
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	427

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEQINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIR SRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCF IRSNSASPDLGILFELGISYIRNSTGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGS VFYQIMTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPM LLEQPDVMDALRSSWAGKESTLKRSEKLSKPVSPREGKKKWPELYHILKTMHCSCLPCYKIMRDKEFLKSTFLLVYHDCV LPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	NM_001374257
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	427

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEQINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIR SRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCF IRSNSASPDLGILFELGISYIRNSTGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGS VFYQIMTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPM LLEQPDVMDALRSSWAGKESTLKRSEKLSKPVSPREGKKKWPELYHILKTMHCSCLPCYKIMVITNPNLL*

Gene Symbol:	NPHP1
Accession:	NM_000272
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	483

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQSRGRIFLVSKPVLQQINTVDV LTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMS IQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNS TGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQIMTMRRQPQLLVKLRSLNRR SRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKR SEKRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQ TYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	NM_001374256
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	426

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIRS RPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFI RSNSASPDLGILFELGISYIRNSTGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSV FYQIMTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPML LEQPDVMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQE NQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	NM_001128178
Location:	EXON
Amino Acid Prediction:	E to Q (nonsynonymous)
Amino Acid Position:	427

Amino Acid Sequence (Calculated using NCBI transcript definition)
MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENKNALQKLSKADESAPVANYNQ RKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEESESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAV GDFTAQQVGDLTFKKGEILLVIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV KQRTDPHWSAVQKAISEQINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQLAFRDLMWDATEGTIR SRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSNIHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCF IRSNSASPDLGILFELGISYIRNSTGQRGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGS VFYQIMTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQSTDLISHPMLATFPM LLEQPDVMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCVLPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQ ENQGALQALLSPDGVHEPFDLSEQTYDFLGEMRKNAV*

Gene Symbol:	NPHP1
Accession:	XM_006712552
Location:	INTRON

Variant Samples

ClinVar GRCh37

ClinVar GRCh38

Additional Information

External Database Links

Database	Acc Id	Source(s)
ClinVar	RCV000293428	CLINVAR
	RCV000334175	CLINVAR
	RCV000381757	CLINVAR
dbSNP (RS)	rs886054753	CLINVAR
MedGen	C1846790	CLINVAR
	C1855681	CLINVAR
	C4551559	CLINVAR
NCBI Gene	NPHP1	CLINVAR
OMIM	256100	CLINVAR
	266900	CLINVAR
	607100	CLINVAR
	609583	CLINVAR

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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Variant: RGD:11650507 - Homo sapiens

Imported Disease Annotations - ClinVar