FAM47C

family with sequence similarity 47 member C

Basic information

Region (hg38): X:37008366-37011664

Links

ENSG00000198173 ∙ NCBI:442444 ∙ OMIM:301067 ∙ HGNC:25301 ∙ Uniprot:Q5HY64 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM47C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM47C gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5		5
missense			81	4		85
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	81	9	0

Variants in FAM47C

This is a list of pathogenic ClinVar variants found in the FAM47C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-37008418-A-T		not specified	Uncertain significance (Nov 03, 2022)
X-37008426-C-T		not specified	Uncertain significance (Aug 01, 2024)
X-37008427-C-T		not specified	Uncertain significance (Jan 31, 2022)
X-37008435-C-T		not specified	Uncertain significance (Jan 31, 2022)
X-37008439-C-T		not specified	Uncertain significance (Jan 31, 2022)
X-37008443-T-G		not specified	Uncertain significance (Jan 31, 2022)
X-37008463-C-A		not specified	Likely benign (Jan 31, 2022)
X-37008518-G-T		not specified	Uncertain significance (Jan 29, 2024)
X-37008531-C-A		not specified	Uncertain significance (Jul 15, 2021)
X-37008531-C-T		not specified	Uncertain significance (Dec 07, 2024)
X-37008650-A-T		not specified	Uncertain significance (Sep 06, 2022)
X-37008666-C-T		not specified	Uncertain significance (Mar 07, 2024)
X-37008679-C-G		not specified	Uncertain significance (May 27, 2022)
X-37008685-G-A		not specified	Uncertain significance (Sep 16, 2021)
X-37008687-A-G		not specified	Uncertain significance (Jan 03, 2025)
X-37008690-A-C		not specified	Likely benign (Jan 03, 2025)
X-37008747-G-A		not specified	Uncertain significance (Dec 03, 2024)
X-37008763-T-A		not specified	Conflicting classifications of pathogenicity (Dec 20, 2024)
X-37008768-G-C		not specified	Uncertain significance (Mar 11, 2024)
X-37008778-C-T		not specified	Uncertain significance (Jul 02, 2024)
X-37008789-A-G		not specified	Likely benign (Jun 18, 2021)
X-37008832-T-C		not specified	Uncertain significance (Nov 09, 2024)
X-37008865-C-T		not specified	Uncertain significance (Oct 24, 2024)
X-37008885-C-G		not specified	Uncertain significance (Sep 26, 2024)
X-37008929-C-A		not specified	Uncertain significance (Aug 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM47C	protein_coding	protein_coding	ENST00000358047	1	3308

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.534	510	477	1.07	0.0000445	6611
Missense in Polyphen		119	123.16	0.96624		2102
Synonymous	-1.09	210	191	1.10	0.0000177	2301
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 1.76
• rvis_percentile_EVS: 96.75

Haploinsufficiency Scores

• pHI: 0.0371
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0524

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fam47c