VCV002574565.3 - ClinVar

NM_153002.3(GPR156):c.1863dup (p.His622fs)

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.

(2)

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.

Pathogenic/Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_153002.3(GPR156):c.1863dup (p.His622fs)

Variation ID: 2574565 Accession: VCV002574565.3

Type and length

Duplication, 1 bp

Location

Cytogenetic: 3q13.33 3: 120167613-120167614 (GRCh38) [ NCBI UCSC ] 3: 119886460-119886461 (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	Oct 28, 2023	Jun 9, 2024	Oct 26, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_153002.3:c.1863dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_694547.2:p.His622fs	frameshift
NM_153002.3:c.1863dupG MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		frameshift
NM_001168271.2:c.1851dup	NP_001161743.1:p.His618fs	frameshift
NC_000003.12:g.120167617dup
NC_000003.11:g.119886464dup

... more HGVS ... less HGVS

Protein change

H618fs, H622fs

Other names

Canonical SPDI

NC_000003.12:120167613:CCCC:CCCCC

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.

Links

OMIM: 610464.0002 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.
GPR156		-	-	GRCh38 GRCh37	63	83

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.
Hearing loss, autosomal recessive	Likely pathogenic (1)	no assertion criteria provided	May 24, 2023	RCV003447652.1
Hearing loss, autosomal recessive 121	Pathogenic (1)	no assertion criteria provided	Oct 26, 2023	RCV003387447.2

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 pathogenic (May 24, 2023)	no assertion criteria provided Method: research	Hearing loss, autosomal recessive (Autosomal recessive inheritance) Affected status: yes Allele origin: inherited	Mustafa Tekin Lab, University Of Miami, Miller School Of Medicine Accession: SCV004022366.1 First in ClinVar: Dec 17, 2023 Last updated: Dec 17, 2023
Pathogenic (Oct 26, 2023)	no assertion criteria provided Method: literature only	DEAFNESS, AUTOSOMAL RECESSIVE 121 Affected status: not provided Allele origin: germline	OMIM Accession: SCV004098890.2 First in ClinVar: Oct 28, 2023 Last updated: Jun 09, 2024	Publications: PubMed (1) PubMed: 37814107 Comment on evidence: In 2 Turkish sisters (family 2986) with nonsyndromic sensorineural hearing loss (DFNB121; 620551), Ramzan et al. (2023) identified homozygosity for a 1-bp duplication (c.1863dupG, NM_153002.3) … (more) In 2 Turkish sisters (family 2986) with nonsyndromic sensorineural hearing loss (DFNB121; 620551), Ramzan et al. (2023) identified homozygosity for a 1-bp duplication (c.1863dupG, NM_153002.3) in exon 10 of the GPR156 gene, causing a frameshift predicted to result in a premature termination codon (His622AlafsTer30). Their unaffected parents were both heterozygous for the duplication, which was not found in 1,612 in-house Turkish controls or in the gnomAD database. (less)

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

Title	Author	Journal	Year	Link
Novel GPR156 variants confirm its role in moderate sensorineural hearing loss.	Ramzan M	Scientific reports	2023	PMID: 37814107

Text-mined citations for this variant ...

Record last updated Sep 17, 2024

ClinVar Genomic variation as it relates to human health

NM_153002.3(GPR156):c.1863dup (p.His622fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...