NM_172369.5(C1QC):c.490G>A (p.Gly164Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 15, 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:: RCV003546567.2

Allele description [Variation Report for NM_172369.5(C1QC):c.490G>A (p.Gly164Ser)]

NM_172369.5(C1QC):c.490G>A (p.Gly164Ser)

Gene:

C1QC:complement C1q C chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.12

Genomic location:

Preferred name:

NM_172369.5(C1QC):c.490G>A (p.Gly164Ser)

Other names:

C1QC, GLY164SER

HGVS:

NC_000001.11:g.22647535G>A
NG_007565.1:g.8911G>A
NM_001114101.3:c.490G>A
NM_001347619.2:c.490G>A
NM_001347620.2:c.223G>A
NM_172369.5:c.490G>AMANE SELECT
NP_001107573.1:p.Gly164Ser
NP_001334548.1:p.Gly164Ser
NP_001334549.1:p.Gly75Ser
NP_758957.2:p.Gly164Ser
LRG_24t1:c.490G>A
LRG_24:g.8911G>A
NC_000001.10:g.22974028G>A
NM_001114101.1:c.490G>A
NM_001114101.2:c.490G>A

Protein change:

G164S; GLY164SER

Links:

OMIM: 120575.0004; dbSNP: rs752596663

NCBI 1000 Genomes Browser:

rs752596663

Molecular consequence:

NM_001114101.3:c.490G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347619.2:c.490G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001347620.2:c.223G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_172369.5:c.490G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004270592	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 15, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24157463, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004270592

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 15, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Rothmund-Thomson syndrome and glomerulonephritis in a homozygous C1q-deficient patient due to a Gly164Ser C1qC mutation.

López-Lera A, Torres-Canizales JM, Garrido S, Morales A, López-Trascasa M.

J Invest Dermatol. 2014 Apr;134(4):1152-1154. doi: 10.1038/jid.2013.444. Epub 2013 Oct 24. No abstract available.

PubMed [citation]

PMID:: 24157463

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, SCV004270592.1

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 164 of the C1QC protein (p.Gly164Ser). This variant is present in population databases (rs752596663, gnomAD 0.004%). This missense change has been observed in individual(s) with C1QC-related conditions (PMID: 24157463). ClinVar contains an entry for this variant (Variation ID: 440743). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.

#	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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