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NM_006891.4(CRYGD):c.155C>G (p.Ser52Trp) AND Aculeiform cataract

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 31, 2021
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:
RCV002233520.13

Allele description [Variation Report for NM_006891.4(CRYGD):c.155C>G (p.Ser52Trp)]

NM_006891.4(CRYGD):c.155C>G (p.Ser52Trp)

Genes:
CRYGD:crystallin gamma D [Gene - OMIM - HGNC]
LOC100507443:uncharacterized LOC100507443 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
2q33.3
Genomic location:
Preferred name:
NM_006891.4(CRYGD):c.155C>G (p.Ser52Trp)
HGVS:
  • NC_000002.12:g.208124209G>C
  • NG_008039.1:g.5381C>G
  • NM_006891.4:c.155C>GMANE SELECT
  • NP_008822.2:p.Ser52Trp
  • NC_000002.11:g.208988933G>C
  • NM_006891.3:c.155C>G
Protein change:
S52W
Links:
dbSNP: rs762200707
NCBI 1000 Genomes Browser:
rs762200707
Molecular consequence:
  • NM_006891.4:c.155C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Aculeiform cataract (CTRCT4)
Synonyms:
Fasciculiform cataract; Frosted cataract; Needle-shaped cataract
Identifiers:
MedGen: C1861832; Human Phenotype Ontology: HP:0010926

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000766136Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 31, 2021) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation.

Kobayashi Y, Yang S, Nykamp K, Garcia J, Lincoln SE, Topper SE.

Genome Med. 2017 Feb 6;9(1):13. doi: 10.1186/s13073-017-0403-7.

PubMed [citation]
PMID:
28166811
PMCID:
PMC5295186

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, SCV000766136.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces serine with tryptophan at codon 52 of the CRYGD protein (p.Ser52Trp). The serine residue is weakly conserved and there is a large physicochemical difference between serine and tryptophan. This variant is present in population databases (rs762200707, ExAC 0.07%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has not been reported in the literature in individuals affected with CRYGD-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024