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NM_000112.4(SLC26A2):c.1950del (p.Ile651fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 6, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001236938.8

Allele description [Variation Report for NM_000112.4(SLC26A2):c.1950del (p.Ile651fs)]

NM_000112.4(SLC26A2):c.1950del (p.Ile651fs)

Gene:
SLC26A2:solute carrier family 26 member 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_000112.4(SLC26A2):c.1950del (p.Ile651fs)
HGVS:
  • NC_000005.10:g.149981543del
  • NG_007147.2:g.22661del
  • NM_000112.4:c.1950delMANE SELECT
  • NP_000103.2:p.Ile651fs
  • LRG_684t1:c.1950del
  • LRG_684:g.22661del
  • NC_000005.9:g.149361106del
  • NM_000112.3:c.1950del
Protein change:
I651fs
Links:
dbSNP: rs774648833
NCBI 1000 Genomes Browser:
rs774648833
Molecular consequence:
  • NM_000112.4:c.1950del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Achondrogenesis, type IB (ACG1B)
Synonyms:
Achondrogenesis Fraccaro type
Identifiers:
MONDO: MONDO:0010966; MedGen: C0265274; Orphanet: 932; Orphanet: 93298; OMIM: 600972
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
Name:
Multiple epiphyseal dysplasia type 4 (EDM4)
Synonyms:
Multiple epiphyseal dysplasia, autosomal recessive; Multiple epiphyseal dysplasia with clubfoot; Multiple epiphyseal dysplasia with double-layered patella; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009189; MedGen: C1847593; Orphanet: 93307; OMIM: 226900
Name:
Diastrophic dysplasia (DTD)
Synonyms:
Diastrophic dwarfism
Identifiers:
MONDO: MONDO:0009107; MedGen: C0220726; Orphanet: 628; OMIM: 222600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001409679Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Apr 6, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001409679.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the SLC26A2 protein in which other variant(s) (p.Ala715Val) have been determined to be pathogenic (PMID: 11448940, 15294877, 21077204). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 962984). This variant has not been reported in the literature in individuals affected with SLC26A2-related conditions. This variant is present in population databases (rs774648833, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Ile651Leufs*9) in the SLC26A2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 89 amino acid(s) of the SLC26A2 protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024