NM_174978.3(C14orf39):c.1232_1234del (p.Val411del) AND Inherited primary ovarian failure

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 3, 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:: RCV003994698.1

Allele description [Variation Report for NM_174978.3(C14orf39):c.1232_1234del (p.Val411del)]

NM_174978.3(C14orf39):c.1232_1234del (p.Val411del)

Gene:

C14orf39:chromosome 14 open reading frame 39 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q23.1

Genomic location:

Preferred name:

NM_174978.3(C14orf39):c.1232_1234del (p.Val411del)

HGVS:

NC_000014.9:g.60457043_60457045del
NM_174978.3:c.1232_1234delMANE SELECT
NP_777638.3:p.Val411del
NC_000014.8:g.60923761_60923763del
NM_174978.3:c.1232_1234delTAGMANE SELECT

Protein change:

V411del

Molecular consequence:

NM_174978.3:c.1232_1234del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Inherited primary ovarian failure
Synonyms:: Premature ovarian failure, familial; Idiopathic familial premature ovarian failure
Identifiers:: MONDO: MONDO:0019852; MedGen: C2930861; OMIM: PS311360

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004812685	Molecular Genetics, Royal Melbourne Hospital See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 3, 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

SCV004812685

Molecular Genetics, Royal Melbourne Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 3, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Molecular Genetics, Royal Melbourne Hospital, SCV004812685.1

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

Description

This sequence change is predicted to cause a change in the length of the protein due to an in-frame deletion of one amino acid in a non-repeat region of the C14orf39 protein, p.(Val411del). The region deleted is weakly conserved (100 vertebrates, UCSC), and is not located in an annotated domain. The highest population minor allele frequency in gnomAD v2.1 is 0.0008% (1/127,796 alleles) in the European (non-Finnish) population, which is consistent with recessive disease. To our knowledge, this variant has not been reported in the literature in any individuals with premature ovarian insufficiency. Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PM2_Supporting, PM4_Supporting.

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

Last Updated: Apr 20, 2024

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