VCV000879291.5 - ClinVar

NM_001368894.2(PAX6):c.511G>A (p.Gly171Ser)

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Uncertain significance

4 out of 4 submissions contributed to this 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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001368894.2(PAX6):c.511G>A (p.Gly171Ser)

Variation ID: 879291 Accession: VCV000879291.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11p13 11: 31800745 (GRCh38) [ NCBI UCSC ] 11: 31822293 (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	May 31, 2020	May 31, 2020	Jan 13, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_001368894.2:c.511G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001355823.1:p.Gly171Ser	missense
NM_000280.6:c.469G>A	NP_000271.1:p.Gly157Ser	missense
NM_001127612.3:c.469G>A	NP_001121084.1:p.Gly157Ser	missense
NM_001258462.3:c.511G>A	NP_001245391.1:p.Gly171Ser	missense
NM_001258463.2:c.511G>A	NP_001245392.1:p.Gly171Ser	missense
NM_001258464.2:c.469G>A	NP_001245393.1:p.Gly157Ser	missense
NM_001258465.3:c.469G>A	NP_001245394.1:p.Gly157Ser	missense
NM_001310158.2:c.511G>A	NP_001297087.1:p.Gly171Ser	missense
NM_001310159.1:c.469G>A	NP_001297088.1:p.Gly157Ser	missense
NM_001310160.2:c.61G>A	NP_001297089.1:p.Gly21Ser	missense
NM_001310161.3:c.61G>A	NP_001297090.1:p.Gly21Ser	missense
NM_001368887.2:c.469G>A	NP_001355816.1:p.Gly157Ser	missense
NM_001368888.2:c.469G>A	NP_001355817.1:p.Gly157Ser	missense
NM_001368889.2:c.469G>A	NP_001355818.1:p.Gly157Ser	missense
NM_001368890.2:c.469G>A	NP_001355819.1:p.Gly157Ser	missense
NM_001368891.2:c.469G>A	NP_001355820.1:p.Gly157Ser	missense
NM_001368892.2:c.511G>A	NP_001355821.1:p.Gly171Ser	missense
NM_001368893.2:c.511G>A	NP_001355822.1:p.Gly171Ser	missense
NM_001368899.2:c.61G>A	NP_001355828.1:p.Gly21Ser	missense
NM_001368900.2:c.61G>A	NP_001355829.1:p.Gly21Ser	missense
NM_001368901.2:c.61G>A	NP_001355830.1:p.Gly21Ser	missense
NM_001368902.2:c.61G>A	NP_001355831.1:p.Gly21Ser	missense
NM_001368903.2:c.61G>A	NP_001355832.1:p.Gly21Ser	missense
NM_001368904.2:c.61G>A	NP_001355833.1:p.Gly21Ser	missense
NM_001368905.2:c.61G>A	NP_001355834.1:p.Gly21Ser	missense
NM_001368906.2:c.61G>A	NP_001355835.1:p.Gly21Ser	missense
NM_001368907.2:c.61G>A	NP_001355836.1:p.Gly21Ser	missense
NM_001368908.2:c.61G>A	NP_001355837.1:p.Gly21Ser	missense
NM_001368909.2:c.61G>A	NP_001355838.1:p.Gly21Ser	missense
NM_001368910.2:c.712G>A	NP_001355839.1:p.Gly238Ser	missense
NM_001368911.2:c.514G>A	NP_001355840.1:p.Gly172Ser	missense
NM_001368912.2:c.511G>A	NP_001355841.1:p.Gly171Ser	missense
NM_001368913.2:c.511G>A	NP_001355842.1:p.Gly171Ser	missense
NM_001368914.2:c.511G>A	NP_001355843.1:p.Gly171Ser	missense
NM_001368915.2:c.469G>A	NP_001355844.1:p.Gly157Ser	missense
NM_001368916.2:c.469G>A	NP_001355845.1:p.Gly157Ser	missense
NM_001368917.2:c.469G>A	NP_001355846.1:p.Gly157Ser	missense
NM_001368918.2:c.586G>A	NP_001355847.1:p.Gly196Ser	missense
NM_001368919.2:c.586G>A	NP_001355848.1:p.Gly196Ser	missense
NM_001368920.2:c.544G>A	NP_001355849.1:p.Gly182Ser	missense
NM_001368921.2:c.310G>A	NP_001355850.1:p.Gly104Ser	missense
NM_001368922.2:c.310G>A	NP_001355851.1:p.Gly104Ser	missense
NM_001368923.2:c.310G>A	NP_001355852.1:p.Gly104Ser	missense
NM_001368924.2:c.310G>A	NP_001355853.1:p.Gly104Ser	missense
NM_001368925.2:c.310G>A	NP_001355854.1:p.Gly104Ser	missense
NM_001368926.2:c.310G>A	NP_001355855.1:p.Gly104Ser	missense
NM_001368927.2:c.310G>A	NP_001355856.1:p.Gly104Ser	missense
NM_001368928.2:c.268G>A	NP_001355857.1:p.Gly90Ser	missense
NM_001368929.2:c.61G>A	NP_001355858.1:p.Gly21Ser	missense
NM_001604.6:c.511G>A	NP_001595.2:p.Gly171Ser	missense
NR_160916.2:n.933G>A		non-coding transcript variant
NR_160917.2:n.938G>A		non-coding transcript variant
NC_000011.10:g.31800745C>T
NC_000011.9:g.31822293C>T
NG_008679.1:g.22217G>A
LRG_720:g.22217G>A

... more HGVS ... less HGVS

Protein change

G104S, G196S, G172S, G21S, G238S, G90S, G182S, G157S, G171S

Other names

Canonical SPDI

NC_000011.10:31800744:C:T

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.

Links

ClinGen: CA379958048 dbSNP: rs1953501315 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	826	1039

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.
Autosomal dominant keratitis	Uncertain significance (1)	criteria provided, single submitter	Jan 13, 2018	RCV001106653.5
Anophthalmia-microphthalmia syndrome	Uncertain significance (1)	criteria provided, single submitter	Jan 13, 2018	RCV001106652.5
Foveal hypoplasia 1	Uncertain significance (1)	criteria provided, single submitter	Jan 13, 2018	RCV001106654.5
carboxymethyl-dextran-A2-gadolinium-DOTA	Uncertain significance (1)	criteria provided, single submitter	Jan 13, 2018	RCV001108805.5

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.	Expand all rows Collapse all rows 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.
Uncertain significance (Jan 13, 2018) C Contributing to aggregate classification	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Anophthalmia-microphthalmia syndrome	Illumina Laboratory Services, Illumina Accession: SCV001263733.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: show This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Jan 13, 2018) C Contributing to aggregate classification	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Autosomal dominant keratitis	Illumina Laboratory Services, Illumina Accession: SCV001263734.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: show This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Jan 13, 2018) C Contributing to aggregate classification	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Foveal hypoplasia 1	Illumina Laboratory Services, Illumina Accession: SCV001263735.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: show This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Uncertain significance (Jan 13, 2018) C Contributing to aggregate classification	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	carboxymethyl-dextran-A2-gadolinium-DOTA	Illumina Laboratory Services, Illumina Accession: SCV001266086.1 First in ClinVar: May 31, 2020 Last updated: May 31, 2020	Comment: show This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Comment:

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

Comment:

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 rs1953501315 ...

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 Apr 13, 2026