NM_005157.6(ABL1):c.311C>G (p.Thr104Ser) AND Congenital heart defects and skeletal malformations syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 17, 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:: RCV003458814.1

Allele description [Variation Report for NM_005157.6(ABL1):c.311C>G (p.Thr104Ser)]

NM_005157.6(ABL1):c.311C>G (p.Thr104Ser)

Gene:

ABL1:ABL proto-oncogene 1, non-receptor tyrosine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.12

Genomic location:

Preferred name:

NM_005157.6(ABL1):c.311C>G (p.Thr104Ser)

HGVS:

NC_000009.12:g.130854858C>G
NG_012034.1:g.145978C>G
NM_005157.6:c.311C>GMANE SELECT
NM_007313.3:c.368C>G
NP_005148.2:p.Thr104Ser
NP_009297.2:p.Thr123Ser
LRG_769t1:c.311C>G
LRG_769t2:c.368C>G
LRG_769:g.145978C>G
LRG_769p1:p.Thr104Ser
LRG_769p2:p.Thr123Ser
NC_000009.11:g.133730245C>G

Protein change:

T104S

Links:

dbSNP: rs2132957851

NCBI 1000 Genomes Browser:

rs2132957851

Molecular consequence:

NM_005157.6:c.311C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007313.3:c.368C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Congenital heart defects and skeletal malformations syndrome
Identifiers:: MONDO: MONDO:0060532; MedGen: C4539857; OMIM: 617602

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004176979	Clinical Genomics Laboratory, Washington University in St. Louis	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 17, 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

SCV004176979

Clinical Genomics Laboratory, Washington University in St. Louis

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 17, 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Clinical Genomics Laboratory, Washington University in St. Louis, SCV004176979.1

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

Description

The ABL1 c.311C>G (p.Thr104Ser) variant, to our knowledge, has not been reported in the medical literature This variant has been reported in the ClinVar database as a germline variant of uncertain significance by one submitter. This variant is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. Computational predictors suggest that the variant does not impact ABL1 function. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

#	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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