NM_002968.3(SALL1):c.3005_3008del (p.Ala1002fs) AND Townes syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 23, 2018
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:: RCV000821059.1

Allele description [Variation Report for NM_002968.3(SALL1):c.3005_3008del (p.Ala1002fs)]

NM_002968.3(SALL1):c.3005_3008del (p.Ala1002fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

16q12.1

Genomic location:

Preferred name:

NM_002968.3(SALL1):c.3005_3008del (p.Ala1002fs)

HGVS:

NC_000016.10:g.51139216_51139219del
NG_007990.1:g.17056_17059del
NM_001127892.2:c.2714_2717del
NM_002968.3:c.3005_3008delMANE SELECT
NP_001121364.1:p.Ala905fs
NP_002959.2:p.Ala1002fs
LRG_674:g.17056_17059del
NC_000016.9:g.51173127_51173130del
NM_002968.2:c.3005_3008delCTTG

Protein change:

A1002fs

Links:

dbSNP: rs1597228188

NCBI 1000 Genomes Browser:

rs1597228188

Molecular consequence:

NM_001127892.2:c.2714_2717del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002968.3:c.3005_3008del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000961800	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 23, 2018)	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

SCV000961800

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 23, 2018)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000961800.1

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

Description

This sequence change results in a premature translational stop signal in the SALL1 gene (p.Ala1002Valfs*42). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 323 amino acids of the SALL1 protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SALL1-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant disrupts the C-terminus of the SALL1 protein. Other variant(s) that disrupt this region (p.Cys1139Trpfs*35) have been determined to be pathogenic (PMID:Â¬â€ 16971658, 23894113, 19429598, 18000979,Â¬â€ 23894113, 17221874). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. For these reasons, this variant has been classified as Pathogenic.

#	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: Aug 5, 2023

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