NM_016366.3(CABP2):c.590T>C (p.Ile197Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 13, 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:: RCV000825873.5

Allele description [Variation Report for NM_016366.3(CABP2):c.590T>C (p.Ile197Thr)]

NM_016366.3(CABP2):c.590T>C (p.Ile197Thr)

Gene:

CABP2:calcium binding protein 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_016366.3(CABP2):c.590T>C (p.Ile197Thr)

HGVS:

NC_000011.10:g.67519840A>G
NG_032982.1:g.8589T>C
NM_001318496.2:c.608T>C
NM_016366.3:c.590T>CMANE SELECT
NP_001305425.1:p.Ile203Thr
NP_057450.2:p.Ile197Thr
NC_000011.9:g.67287311A>G
NM_016366.2:c.590T>C
p.Ile197Thr

Protein change:

I197T

Links:

dbSNP: rs145369252

NCBI 1000 Genomes Browser:

rs145369252

Molecular consequence:

NM_001318496.2:c.608T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_016366.3:c.590T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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CASC2 cancer susceptibility 2 [Homo sapiens]
CASC2 cancer susceptibility 2 [Homo sapiens]
Gene ID:255082

Gene
Gene Links for GEO Profiles (Select 41719189) (1)
Gene
Homo sapiens RALBP1 associated Eps domain containing 2 (REPS2), RefSeqGene on ch...
Homo sapiens RALBP1 associated Eps domain containing 2 (REPS2), RefSeqGene on chromosome X
gi|2310187552|ref|NG_012557.2|

Nucleotide
MYD88 NP_002459.2:p.L265P
MYD88 NP_002459.2:p.L265P

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000967358	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Sep 13, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26445815, 24033266

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000967358

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Sep 13, 2018)

germline

clinical testing

PubMed (2)
[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	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran.

Sloan-Heggen CM, Babanejad M, Beheshtian M, Simpson AC, Booth KT, Ardalani F, Frees KL, Mohseni M, Mozafari R, Mehrjoo Z, Jamali L, Vaziri S, Akhtarkhavari T, Bazazzadegan N, Nikzat N, Arzhangi S, Sabbagh F, Otukesh H, Seifati SM, Khodaei H, Taghdiri M, Meyer NC, et al.

J Med Genet. 2015 Dec;52(12):823-9. doi: 10.1136/jmedgenet-2015-103389. Epub 2015 Oct 7.

PubMed [citation]

PMID:: 26445815
PMCID:: PMC4733363

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000967358.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

The p.Ile197Thr variant in CABP2 has been reported in the homozygous state in 1 individual with hearing loss (Sloan-Heggen 2015). It has also been identified in 0.05% (66/126628) of European chromosomes by the Genome Aggregation Database (g nomAD, http://gnomad.broadinstitute.org/). Computational prediction tools and co nservation analysis do not provide strong support for or against an impact to th e protein. In summary, the clinical significance of the p.Ile197Thr variant is u ncertain. ACMG/AMP Criteria applied: PM3_Supporting, PM2_Supporting.

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

Last Updated: Feb 20, 2024

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