Variant Detail

Variant Information
ID
DPV: 10715
Chromosome
9
Gene
HGVS (GRCh37/hg19)
NC_000009.11:g.127262965G>A
HGVS (GRCh38/hg38)
NC_000009.12:g.124500686G>A
HGVS (RNA)
NM_004959.4:c.274C>T
HGVS (Protein)
NP_004950.2:p.R92W
dbSNP
-
ClinGen Allele Registry
CA10588831
Allele Frequency
Individual Information

ID
DPVS:11228.2
Clinical Significance
Pathogenic
Date Last Evaluated
2019-07-11
Clinical Significance Citation
Igarashi, M. Identical NR5A1 Missense Mutations in Two Unrelated 46,XX Individuals with Testicular Tissues. 2017 Hum Mutat. 2017 Jan;38(1):39-42. doi: 10.1002/humu.23116. Epub 2016 Sep 21. PMID:27610946

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
paternal
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
46XX karyotype/ Patient  carried additional substitution in FOXL2 (NM_023067.3; c.1045C>G, r.1045u>g, p.Arg349Gly)

ID
DPVS:11229.2
Clinical Significance
Pathogenic
Date Last Evaluated
2019-07-11
Clinical Significance Citation
Igarashi, M. Identical NR5A1 Missense Mutations in Two Unrelated 46,XX Individuals with Testicular Tissues. 2017 Hum Mutat. 2017 Jan;38(1):39-42. doi: 10.1002/humu.23116. Epub 2016 Sep 21. PMID:27610946

Transcript
-
Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
46XX karyotype/Patient  had a mutation in POR (NM_000941.2; c.1370G>A, r.1370g>a, p.Arg457His)

ID
DPVS:12489.1
Clinical Significance
Likely pathogenic
Date Last Evaluated
2020-01-08
Clinical Significance Citation
Saito-Hakoda, A. A Follow-Up from Infancy to Puberty in a Japanese Male with SRY-Negative 46,XX Testicular Disorder of Sex Development Carrying a p.Arg92Trp Mutation in NR5A1. 2019 Sex Dev. 2019;13(2):60-66. doi: 10.1159/000496777. Epub 2019 Feb 9. PMID:30739115
Igarashi, M. Identical NR5A1 Missense Mutations in Two Unrelated 46,XX Individuals with Testicular Tissues. 2017 Hum Mutat. 2017 Jan;38(1):39-42. doi: 10.1002/humu.23116. Epub 2016 Sep 21. PMID:27610946

Transcript
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Disease

hypergonadotropic hypogonadism

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
NM_004959.4:c.[274C>T]|Double mutations

ClinVar
Model Animals
VCF
VCF (GRCh37/hg19) 
											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
9	127262965	NC_000009.11:g.127262965G>A	G	A	.	.	CLNALLELEID=260482;CLNDN=46,XY_sex_reversal,_type_3|46,XX_sex_reversal_4;CLNDISDB=MONDO:MONDO:0013066,MedGen:C3489793,OMIM:612965|MONDO:MONDO:0060489,MedGen:C4479552,OMIM:617480;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000009.11:g.127262965G>A;GENEINFO=7983:2516;DPVID=10715;DPVSIG=Likely_pathogenic|Pathogenic;DPVDSDBID=OMIM:617480|OMIM:612965;DPVDBN=46\x2cXX_sex_reversal_4|46\x2cXY_sex_reversal_3;DPVHGVS=NC_000009.11:g.127262965G>A	.
VCF (GRCh38/hg38) 
											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-ri3_lyiw>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
9	124500686	NC_000009.11:g.127262965G>A	G	A	.	.	dbSNP_RSID=rs886039769;CLNALLELEID=260482;CLNDN=46,XY_sex_reversal,_type_3|46,XX_sex_reversal_4;CLNDISDB=MONDO:MONDO:0013066,MedGen:C3489793,OMIM:612965|MONDO:MONDO:0060489,MedGen:C4479552,OMIM:617480;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000009.12:g.124500686G>A;GENEINFO=7983:2516;DPVID=10715;DPVSIG=Likely_pathogenic|Pathogenic;DPVDSDBID=OMIM:617480|OMIM:612965;DPVDBN=46\x2cXX_sex_reversal_4|46\x2cXY_sex_reversal_3;DPVHGVS=NC_000009.12:g.124500686G>A	.