NM_133261.3(GIPC3):c.122C>A (p.Thr41Lys) AND Autosomal recessive nonsyndromic hearing loss 15

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004700476.2

Allele description [Variation Report for NM_133261.3(GIPC3):c.122C>A (p.Thr41Lys)]

NM_133261.3(GIPC3):c.122C>A (p.Thr41Lys)

Gene:

GIPC3:GIPC PDZ domain containing family member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_133261.3(GIPC3):c.122C>A (p.Thr41Lys)

HGVS:

NC_000019.10:g.3585719C>A
NG_031943.1:g.5149C>A
NM_133261.3:c.122C>AMANE SELECT
NP_573568.1:p.Thr41Lys
NC_000019.9:g.3585717C>A
NM_133261.2:c.122C>A

Protein change:

T41K

Links:

dbSNP: rs727503062

NCBI 1000 Genomes Browser:

rs727503062

Molecular consequence:

NM_133261.3:c.122C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Autosomal recessive nonsyndromic hearing loss 15
Synonyms:: DEAFNESS, AUTOSOMAL RECESSIVE 15; DEAFNESS, AUTOSOMAL RECESSIVE 72; DEAFNESS, AUTOSOMAL RECESSIVE 95
Identifiers:: MONDO: MONDO:0011160; MedGen: C1866094; Orphanet: 90636; OMIM: 601869

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000992247	Kariminejad - Najmabadi Pathology & Genetics Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic Score: 25741868 (Jun 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005871090	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 1, 2024)	biparental	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000992247

Kariminejad - Najmabadi Pathology & Genetics Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
Score: 25741868
(Jun 17, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005871090

Daryl Scott Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 1, 2024)

biparental

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	biparental	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Kariminejad - Najmabadi Pathology & Genetics Center, SCV000992247.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Now, we have found stronger evidence of pathogenicity and changed this variant classification from uncertain significance to likely pathogenic (PM2,PM3_Moderate ,PP3_Moderate; according to ACMG Guidelines, 2015)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Daryl Scott Lab, Baylor College of Medicine, SCV005871090.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

PS4, PM2, PP1, PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	biparental	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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