NM_002968.3(SALL1):c.2929G>A (p.Ala977Thr) AND Townes syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 28, 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:: RCV003595195.2

Allele description [Variation Report for NM_002968.3(SALL1):c.2929G>A (p.Ala977Thr)]

NM_002968.3(SALL1):c.2929G>A (p.Ala977Thr)

Gene:

SALL1:spalt like transcription factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q12.1

Genomic location:

Preferred name:

NM_002968.3(SALL1):c.2929G>A (p.Ala977Thr)

HGVS:

NC_000016.10:g.51139293C>T
NG_007990.1:g.16980G>A
NM_001127892.2:c.2638G>A
NM_002968.3:c.2929G>AMANE SELECT
NP_001121364.1:p.Ala880Thr
NP_002959.2:p.Ala977Thr
NP_002959.2:p.Ala977Thr
LRG_674t1:c.2929G>A
LRG_674:g.16980G>A
LRG_674p1:p.Ala977Thr
NC_000016.9:g.51173204C>T
NM_002968.2:c.2929G>A

Protein change:

A880T

Molecular consequence:

NM_001127892.2:c.2638G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002968.3:c.2929G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Townes syndrome (TBS)
Synonyms:: Townes-Brocks syndrome
Identifiers:: MONDO: MONDO:0007142; MeSH: C536974; MedGen: C0265246; Orphanet: 857; OMIM: PS107480

Recent activity

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USP13 ubiquitin specific peptidase 13 [Bos taurus]
USP13 ubiquitin specific peptidase 13 [Bos taurus]
Gene ID:100141289

Gene
100141289[uid] AND (alive[prop]) (1)
Gene
BJ100361 NIBB Mochii normalized Xenopus early gastrula library Xenopus laevis cD...
BJ100361 NIBB Mochii normalized Xenopus early gastrula library Xenopus laevis cDNA clone XL152g23 3', mRNA sequence
gi|17603076|gnl|dbEST|10568684|dbj| 361.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004269445	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 28, 2023)	germline	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

SCV004269445

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 28, 2023)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004269445.1

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

Description

The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 977 of the SALL1 protein (p.Ala977Thr). This variant has not been reported in the literature in individuals affected with SALL1-related conditions. 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 SALL1 protein function. 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.

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

Last Updated: Sep 29, 2024

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