FAM47C

protein-coding

family with sequence similarity 47 member C

Gene summary

This gene encodes a product belonging to a family of proteins with unknown function. The coding sequence of this family member includes several tandemly repeated regions. [provided by RefSeq, Sep 2011]

MANE transcript

NM_001013736.3

Inheritance

ClinVar variants

U:156B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:37,008,366-37,011,664

External References & Databases

Ensembl (ENSG00000198173)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

male infertility with azoospermia or oligozoospermia due to single gene mutationMODERATE

Inheritance Pattern: XL

Disease ID:MONDO:0018393

Submitter: King Faisal Specialist Hospital and Research Center

Alhathal et al., 2020 (PMID: 32719396) reported a missense variant in a large male infertility cohort (n=285 infertile man and case–control fertile man). Gene is scored according to ClinGen classification. Moderate based on, reported in male infertility (PMID: 30922974)/ Expression (PMID: 18454149)/ (>1 independent study with several unrelated probands with pathogenic variants, supporting experimental data and no contradictory evidences).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM47C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 162

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001013736.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				7 clinvar		7
missense			155 clinvar	7 clinvar		162
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	156	14	0	170

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001013736.3	RefSeq	NP_001013758.1	1	MANE Select
ENST00000358047.5	Ensembl	ENSP00000367913.3	1	MANE Select

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358047
Coding exons: 1
Length: 3308

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.714
RVIS EVS: 1.76
RVIS percentile EVS: 96.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0524

Gene Damage Prediction

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