NM_031942.5(CDCA7):c.1148G>A (p.Arg383His) AND Immunodeficiency-centromeric instability-facial anomalies syndrome 3

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 5, 2022
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:: RCV000210909.6

Allele description [Variation Report for NM_031942.5(CDCA7):c.1148G>A (p.Arg383His)]

NM_031942.5(CDCA7):c.1148G>A (p.Arg383His)

Gene:

CDCA7:cell division cycle associated 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q31.1

Genomic location:

Preferred name:

NM_031942.5(CDCA7):c.1148G>A (p.Arg383His)

HGVS:

NC_000002.12:g.173366395G>A
NG_047202.1:g.17379G>A
NM_031942.5:c.1148G>AMANE SELECT
NM_145810.3:c.911G>A
NP_114148.3:p.Arg383His
NP_665809.1:p.Arg304His
NC_000002.11:g.174231123G>A
NM_145810.2:c.911G>A

Protein change:

R304H; ARG304HIS

Links:

OMIM: 609937.0003; dbSNP: rs772929976

NCBI 1000 Genomes Browser:

rs772929976

Molecular consequence:

NM_031942.5:c.1148G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_145810.3:c.911G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Immunodeficiency-centromeric instability-facial anomalies syndrome 3 (ICF3)
Identifiers:: MONDO: MONDO:0014828; MedGen: C4310799; Orphanet: 2268; OMIM: 616910

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267584	OMIM	no assertion criteria provided	Pathogenic (Apr 5, 2019)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV003831015	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 5, 2022)	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

SCV000267584

OMIM

no assertion criteria provided

Pathogenic
(Apr 5, 2019)

germline

literature only

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

SCV003831015

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 5, 2022)

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome.

Thijssen PE, Ito Y, Grillo G, Wang J, Velasco G, Nitta H, Unoki M, Yoshihara M, Suyama M, Sun Y, Lemmers RJ, de Greef JC, Gennery A, Picco P, Kloeckener-Gruissem B, Güngör T, Reisli I, Picard C, Kebaili K, Roquelaure B, Iwai T, Kondo I, et al.

Nat Commun. 2015 Jul 28;6:7870. doi: 10.1038/ncomms8870. Erratum in: Nat Commun. 2016 Jun 22;7:12003. doi: 10.1038/ncomms12003.

PubMed [citation]

PMID:: 26216346
PMCID:: PMC4519989

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 OMIM, SCV000267584.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a French woman, born of consanguineous parents, with immunodeficiency-centromeric instability-facial anomalies syndrome-3 (ICF3; 616910), Thijssen et al. (2015) identified a homozygous c.911G-A transition in exon 8 of the CDCA7 gene, resulting in an arg304-to-his (R304H) substitution at a residue in the conserved C-terminal zinc finger domain. The mutation was found by a combination of homozygosity mapping and whole-exome sequencing and confirmed by Sanger sequencing; it was present at a low frequency (8.24 x 10(-06)) in the ExAC database. Functional studies of the variant were not performed.

#	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		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003831015.2

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

#	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: Oct 8, 2024

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