FAM13C

Gene

family with sequence similarity 13 member C

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

FAM13C1

MANE transcript

NM_198215.4

Inheritance

—

ClinVar variants

U:72B:5

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr10:59,246,130-59,363,181

External References & Databases

Ensembl (ENSG00000148541)

Transcript & Mutation Effects

hg38 • Region Span ~117.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAM13C variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 66

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198215.4. 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						0
missense			65 clinvar	5 clinvar		70
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	72	5	0	77

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198215.4	RefSeq	NP_937858.2	14	MANE Select
ENST00000618804.5	Ensembl	ENSP00000481854.1	14	MANE Select
NM_001001971.3	RefSeq	NP_001001971.1	12	Standard
NM_001143773.1	RefSeq	NP_001137245.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373868
Coding exons: 14
Length: 117050
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.76	237	327	0.726	0.0000177	3856
Missense (PolyPhen)		75	127.75	0.58708		1585
Synonymous	-0.121	127	125	1.01	0.00000741	1093
Loss of Function	3.20	13	32.8	0.396	0.00000174	385

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00018	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0774

Intolerance Scores

RVIS EVS: 0.76
RVIS percentile EVS: 86.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.559

Gene Damage Prediction

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