NM_145054.5(CFAP52):c.1304del (p.Gly435fs) AND Heterotaxy, visceral, 10, autosomal, with male infertility

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 23, 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:: RCV001775181.3

Allele description [Variation Report for NM_145054.5(CFAP52):c.1304del (p.Gly435fs)]

NM_145054.5(CFAP52):c.1304del (p.Gly435fs)

Gene:

CFAP52:cilia and flagella associated protein 52 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_145054.5(CFAP52):c.1304del (p.Gly435fs)

HGVS:

NC_000017.11:g.9633017del
NM_001080556.2:c.1100del
NM_145054.5:c.1304delMANE SELECT
NP_001074025.1:p.Gly367fs
NP_659491.4:p.Gly435fs
NC_000017.10:g.9536334del
NM_145054.4:c.1304del
NM_145054.4:c.1304delG

Protein change:

G367fs

Links:

OMIM: 609804.0002; dbSNP: rs1360832162

NCBI 1000 Genomes Browser:

rs1360832162

Molecular consequence:

NM_001080556.2:c.1100del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145054.5:c.1304del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Heterotaxy, visceral, 10, autosomal, with male infertility
Identifiers:: MONDO: MONDO:0030474; MedGen: C5562072; OMIM: 619607

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002011847	OMIM	no assertion criteria provided	Pathogenic (Nov 5, 2021)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV003836425	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 23, 2022)	unknown	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

SCV002011847

OMIM

no assertion criteria provided

Pathogenic
(Nov 5, 2021)

germline

literature only

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

SCV003836425

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 23, 2022)

unknown

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

Citations

PubMed

CFAP45 deficiency causes situs abnormalities and asthenospermia by disrupting an axonemal adenine nucleotide homeostasis module.

Dougherty GW, Mizuno K, Nöthe-Menchen T, Ikawa Y, Boldt K, Ta-Shma A, Aprea I, Minegishi K, Pang YP, Pennekamp P, Loges NT, Raidt J, Hjeij R, Wallmeier J, Mussaffi H, Perles Z, Elpeleg O, Rabert F, Shiratori H, Letteboer SJ, Horn N, Young S, et al.

Nat Commun. 2020 Nov 2;11(1):5520. doi: 10.1038/s41467-020-19113-0.

PubMed [citation]

PMID:: 33139725
PMCID:: PMC7606486

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, SCV002011847.1

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

Description

In a 15-year-old boy (OI-142) with situs inversus totalis (HTX10; 619607), Dougherty et al. (2020) identified homozygosity for a 1-bp deletion (c.1304delG, NM_145054.4) in the CFAP52 gene, causing a frameshift predicted to result in a premature termination codon (Gly435AlafsTer7). Familial segregation of the variant was not reported. The variant was present at very low minor allele frequency in the 1000 Genomes Project and gnomAD databases (MAF, 0.000004). Immunofluorescence microscopy confirmed that panaxonemal staining of CFAP52, present in control respiratory cilia, was undetectable in respiratory cilia from the proband.

#	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 Baylor Genetics, SCV003836425.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 12, 2024

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