VCV000771097.18 - ClinVar

NM_001368894.2(PAX6):c.537G>C (p.Gly179=)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(4)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001368894.2(PAX6):c.537G>C (p.Gly179=)

Variation ID: 771097 Accession: VCV000771097.18

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11p13 11: 31800719 (GRCh38) [ NCBI UCSC ] 11: 31822267 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 17, 2019	Oct 20, 2024	Jul 1, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001368894.2:c.537G>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001355823.1:p.Gly179=	synonymous
NM_000280.3:c.495G>C
NM_000280.6:c.495G>C	NP_000271.1:p.Gly165=	synonymous
NM_001127612.3:c.495G>C	NP_001121084.1:p.Gly165=	synonymous
NM_001258462.3:c.537G>C	NP_001245391.1:p.Gly179=	synonymous
NM_001258463.2:c.537G>C	NP_001245392.1:p.Gly179=	synonymous
NM_001258464.2:c.495G>C	NP_001245393.1:p.Gly165=	synonymous
NM_001258465.3:c.495G>C	NP_001245394.1:p.Gly165=	synonymous
NM_001310158.2:c.537G>C	NP_001297087.1:p.Gly179=	synonymous
NM_001310159.1:c.495G>C	NP_001297088.1:p.Gly165=	synonymous
NM_001310160.2:c.87G>C	NP_001297089.1:p.Gly29=	synonymous
NM_001310161.3:c.87G>C	NP_001297090.1:p.Gly29=	synonymous
NM_001368887.2:c.495G>C	NP_001355816.1:p.Gly165=	synonymous
NM_001368888.2:c.495G>C	NP_001355817.1:p.Gly165=	synonymous
NM_001368889.2:c.495G>C	NP_001355818.1:p.Gly165=	synonymous
NM_001368890.2:c.495G>C	NP_001355819.1:p.Gly165=	synonymous
NM_001368891.2:c.495G>C	NP_001355820.1:p.Gly165=	synonymous
NM_001368892.2:c.537G>C	NP_001355821.1:p.Gly179=	synonymous
NM_001368893.2:c.537G>C	NP_001355822.1:p.Gly179=	synonymous
NM_001368899.2:c.87G>C	NP_001355828.1:p.Gly29=	synonymous
NM_001368900.2:c.87G>C	NP_001355829.1:p.Gly29=	synonymous
NM_001368901.2:c.87G>C	NP_001355830.1:p.Gly29=	synonymous
NM_001368902.2:c.87G>C	NP_001355831.1:p.Gly29=	synonymous
NM_001368903.2:c.87G>C	NP_001355832.1:p.Gly29=	synonymous
NM_001368904.2:c.87G>C	NP_001355833.1:p.Gly29=	synonymous
NM_001368905.2:c.87G>C	NP_001355834.1:p.Gly29=	synonymous
NM_001368906.2:c.87G>C	NP_001355835.1:p.Gly29=	synonymous
NM_001368907.2:c.87G>C	NP_001355836.1:p.Gly29=	synonymous
NM_001368908.2:c.87G>C	NP_001355837.1:p.Gly29=	synonymous
NM_001368909.2:c.87G>C	NP_001355838.1:p.Gly29=	synonymous
NM_001368910.2:c.738G>C	NP_001355839.1:p.Gly246=	synonymous
NM_001368911.2:c.540G>C	NP_001355840.1:p.Gly180=	synonymous
NM_001368912.2:c.537G>C	NP_001355841.1:p.Gly179=	synonymous
NM_001368913.2:c.537G>C	NP_001355842.1:p.Gly179=	synonymous
NM_001368914.2:c.537G>C	NP_001355843.1:p.Gly179=	synonymous
NM_001368915.2:c.495G>C	NP_001355844.1:p.Gly165=	synonymous
NM_001368916.2:c.495G>C	NP_001355845.1:p.Gly165=	synonymous
NM_001368917.2:c.495G>C	NP_001355846.1:p.Gly165=	synonymous
NM_001368918.2:c.612G>C	NP_001355847.1:p.Gly204=	synonymous
NM_001368919.2:c.612G>C	NP_001355848.1:p.Gly204=	synonymous
NM_001368920.2:c.570G>C	NP_001355849.1:p.Gly190=	synonymous
NM_001368921.2:c.336G>C	NP_001355850.1:p.Gly112=	synonymous
NM_001368922.2:c.336G>C	NP_001355851.1:p.Gly112=	synonymous
NM_001368923.2:c.336G>C	NP_001355852.1:p.Gly112=	synonymous
NM_001368924.2:c.336G>C	NP_001355853.1:p.Gly112=	synonymous
NM_001368925.2:c.336G>C	NP_001355854.1:p.Gly112=	synonymous
NM_001368926.2:c.336G>C	NP_001355855.1:p.Gly112=	synonymous
NM_001368927.2:c.336G>C	NP_001355856.1:p.Gly112=	synonymous
NM_001368928.2:c.294G>C	NP_001355857.1:p.Gly98=	synonymous
NM_001368929.2:c.87G>C	NP_001355858.1:p.Gly29=	synonymous
NM_001604.5:c.537G>C
NM_001604.6:c.537G>C	NP_001595.2:p.Gly179=	synonymous
NR_160916.2:n.959G>C		non-coding transcript variant
NR_160917.2:n.964G>C		non-coding transcript variant
NC_000011.10:g.31800719C>G
NC_000011.9:g.31822267C>G
NG_008679.1:g.22243G>C
LRG_720:g.22243G>C

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000011.10:31800718:C:G

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.00003

Trans-Omics for Precision Medicine (TOPMed) 0.00003

The Genome Aggregation Database (gnomAD), exomes 0.00005

Exome Aggregation Consortium (ExAC) 0.00006

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008

Links

dbSNP: rs374226064 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PAX6		Sufficient evidence for dosage pathogenicity	Little evidence for dosage pathogenicity	GRCh38 GRCh37	695	899

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Likely benign (2)	criteria provided, multiple submitters, no conflicts	Jul 1, 2022	RCV000950347.16
Aniridia 1 Irido-corneo-trabecular dysgenesis	Likely benign (1)	criteria provided, single submitter	Nov 10, 2021	RCV002066261.5
PAX6-related disorder	Likely benign (1)	no assertion criteria provided	Jun 20, 2019	RCV004533644.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely benign (Nov 09, 2018)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001813718.1 First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021
Likely benign (Nov 10, 2021)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Aniridia 1 Irido-corneo-trabecular dysgenesis Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002448644.2 First in ClinVar: Apr 12, 2022 Last updated: Apr 09, 2023
Likely benign (Jul 01, 2022)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004129966.10 First in ClinVar: Nov 20, 2023 Last updated: Oct 20, 2024	Comment: PAX6: BP4, BP7 Number of individuals with the variant: 1
Likely benign (Jun 20, 2019)	no assertion criteria provided Method: clinical testing	PAX6-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004719878.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs374226064 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_001368894.2(PAX6):c.537G>C (p.Gly179=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs374226064 ...