NM_000057.4(BLM):c.3101C>T (p.Thr1034Met) AND Bloom syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 22, 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:: RCV001316694.9

Allele description [Variation Report for NM_000057.4(BLM):c.3101C>T (p.Thr1034Met)]

NM_000057.4(BLM):c.3101C>T (p.Thr1034Met)

Gene:

BLM:BLM RecQ like helicase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q26.1

Genomic location:

Preferred name:

NM_000057.4(BLM):c.3101C>T (p.Thr1034Met)

HGVS:

NC_000015.10:g.90794248C>T
NG_007272.1:g.81877C>T
NM_000057.4:c.3101C>TMANE SELECT
NM_001287246.2:c.3101C>T
NM_001287247.2:c.3101C>T
NM_001287248.2:c.1976C>T
NP_000048.1:p.Thr1034Met
NP_001274175.1:p.Thr1034Met
NP_001274176.1:p.Thr1034Met
NP_001274177.1:p.Thr659Met
LRG_20t1:c.3101C>T
LRG_20:g.81877C>T
NC_000015.9:g.91337478C>T
NM_000057.2:c.3101C>T

Protein change:

T1034M

Links:

dbSNP: rs753652339

NCBI 1000 Genomes Browser:

rs753652339

Molecular consequence:

NM_000057.4:c.3101C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287246.2:c.3101C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287247.2:c.3101C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001287248.2:c.1976C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Bloom syndrome (BLM)
Synonyms:: Bloom-Torre-Machacek syndrome; Growth deficiency, sun-sensitive, telangiectatic, hypo and hyperpigmented skin, predisposition to malignancy and chromosomal instability
Identifiers:: MONDO: MONDO:0008876; MedGen: C0005859; Orphanet: 125; OMIM: 210900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001507326	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002090516	Natera, Inc.	no assertion criteria provided	Uncertain significance (Sep 17, 2018)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001507326

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 2023)

germline

clinical testing

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

SCV002090516

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Sep 17, 2018)

germline

clinical testing

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, SCV001507326.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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 BLM protein function. ClinVar contains an entry for this variant (Variation ID: 485362). This variant has not been reported in the literature in individuals affected with BLM-related conditions. 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 threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 1034 of the BLM protein (p.Thr1034Met).

#	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

From Natera, Inc., SCV002090516.1

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

#	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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