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NM_015139.3(SLC35D1):c.830C>T (p.Thr277Met) AND Schneckenbecken dysplasia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 19, 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:
RCV003601849.1

Allele description

NM_015139.3(SLC35D1):c.830C>T (p.Thr277Met)

Gene:
SLC35D1:solute carrier family 35 member D1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p31.3
Genomic location:
Preferred name:
NM_015139.3(SLC35D1):c.830C>T (p.Thr277Met)
HGVS:
  • NC_000001.11:g.67020415G>A
  • NG_012933.1:g.38983C>T
  • NM_015139.2:c.830C>T
  • NM_015139.3:c.830C>TMANE SELECT
  • NP_055954.1:p.Thr277Met
  • NC_000001.10:g.67486098G>A
Protein change:
T277M
Molecular consequence:
  • NM_015139.3:c.830C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Schneckenbecken dysplasia
Synonyms:
Chondrodysplasia lethal neonatal with snail like pelvis
Identifiers:
MONDO: MONDO:0010013; MedGen: C0432194; Orphanet: 3144; OMIM: 269250

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004547530Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jun 19, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV004547530.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SLC35D1 protein function. This variant has not been reported in the literature in individuals affected with SLC35D1-related conditions. This variant is present in population databases (rs751569615, gnomAD 0.02%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 277 of the SLC35D1 protein (p.Thr277Met).

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

Last Updated: Aug 11, 2024