NM_002968.3(SALL1):c.870_871dup (p.Gln291fs) AND Townes syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 10, 2020
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:: RCV001386756.6

Allele description [Variation Report for NM_002968.3(SALL1):c.870_871dup (p.Gln291fs)]

NM_002968.3(SALL1):c.870_871dup (p.Gln291fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

16q12.1

Genomic location:

Preferred name:

NM_002968.3(SALL1):c.870_871dup (p.Gln291fs)

HGVS:

NC_000016.10:g.51141351GA[3]
NG_007990.1:g.14919TC[3]
NM_001127892.2:c.579_580dup
NM_002968.3:c.870_871dupMANE SELECT
NP_001121364.1:p.Gln194fs
NP_002959.2:p.Gln291fs
LRG_674:g.14919TC[3]
NC_000016.9:g.51175261_51175262insGA
NC_000016.9:g.51175262GA[3]
NM_002968.2:c.870_871dupTC

Protein change:

Q194fs

Links:

dbSNP: rs886041236

NCBI 1000 Genomes Browser:

rs886041236

Molecular consequence:

NM_001127892.2:c.579_580dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_002968.3:c.870_871dup - 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
SCV001587104	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 10, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16088922, 9973281, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001587104

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 10, 2020)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

SALL1 mutation analysis in Townes-Brocks syndrome: twelve novel mutations and expansion of the phenotype.

Botzenhart EM, Green A, Ilyina H, König R, Lowry RB, Lo IF, Shohat M, Burke L, McGaughran J, Chafai R, Pierquin G, Michaelis RC, Whiteford ML, Simola KO, Rösler B, Kohlhase J.

Hum Mutat. 2005 Sep;26(3):282.

PubMed [citation]

PMID:: 16088922

Molecular analysis of SALL1 mutations in Townes-Brocks syndrome.

Kohlhase J, Taschner PE, Burfeind P, Pasche B, Newman B, Blanck C, Breuning MH, ten Kate LP, Maaswinkel-Mooy P, Mitulla B, Seidel J, Kirkpatrick SJ, Pauli RM, Wargowski DS, Devriendt K, Proesmans W, Gabrielli O, Coppa GV, Wesby-van Swaay E, Trembath RC, Schinzel AA, Reardon W, et al.

Am J Hum Genet. 1999 Feb;64(2):435-45.

PubMed [citation]

PMID:: 9973281
PMCID:: PMC1377753

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001587104.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant has not been reported in the literature in individuals with SALL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 279887). For these reasons, this variant has been classified as Pathogenic. This variant is expected to result in a truncated protein lacking all double zinc finger (DZF) domains which are critical for SALL1 protein function (PMID: 16088922, 9973281) This variant is not present in population databases (ExAC no frequency). This sequence change results in a premature translational stop signal in the SALL1 gene (p.Gln291Leufs*24). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1034 amino acids of the SALL1 protein.

#	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: Mar 5, 2024

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