NM_000112.4(SLC26A2):c.1382C>T (p.Ala461Val) AND Atelosteogenesis type II

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 17, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001779964.2

Allele description [Variation Report for NM_000112.4(SLC26A2):c.1382C>T (p.Ala461Val)]

NM_000112.4(SLC26A2):c.1382C>T (p.Ala461Val)

Gene:

SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q32

Genomic location:

Preferred name:

NM_000112.4(SLC26A2):c.1382C>T (p.Ala461Val)

HGVS:

NC_000005.10:g.149980975C>T
NG_007147.2:g.22093C>T
NM_000112.4:c.1382C>TMANE SELECT
NP_000103.2:p.Ala461Val
LRG_684:g.22093C>T
NC_000005.9:g.149360538C>T

Protein change:

A461V

Links:

dbSNP: rs2113698650

NCBI 1000 Genomes Browser:

rs2113698650

Molecular consequence:

NM_000112.4:c.1382C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Atelosteogenesis type II (AO2)
Synonyms:: NEONATAL OSSEOUS DYSPLASIA I; Neonatal osseous dysplasia 1; Atelosteogenesis type 2
Identifiers:: MONDO: MONDO:0009727; MedGen: C1850554; Orphanet: 56304; OMIM: 256050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002015213	Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital	no assertion criteria provided	Likely pathogenic (Nov 17, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002015213

Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital

no assertion criteria provided

Likely pathogenic
(Nov 17, 2021)

germline

clinical testing

Help

Summary from all submissions

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

Details of each submission

From Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, SCV002015213.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	South East Asian	1	not provided	not provided	clinical testing	not provided

Description

This variant has not been identified in gnomAD and 1000g databases. This mis-sense variant is present in compound heterozygous state with another stop gain variant c.532C>T (p.R178X) in SLC26A2 gene. Phenotype observed in the proband was severe shortening of all long bones, exaggerated lumbar lordosis, big toe and radial shortening. Atelosteogenesis II is an autosomal recessive disorder and can be caused by Homozygous or Compound heterozygous mutations. Based on phenotypic overall and identified variant we classify this as likely pathogenic variant.

#	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		1	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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