FAM13C

family with sequence similarity 13 member C

Basic information

Region (hg38): 10:59246129-59363181

Previous symbols: [ "FAM13C1" ]

Links

ENSG00000148541 ∙ NCBI:220965 ∙ ∙ HGNC:19371 ∙ Uniprot:Q8NE31 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM13C gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM13C 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						0
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in FAM13C

This is a list of pathogenic ClinVar variants found in the FAM13C region.

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

Position	Type	Phenotype	Significance	ClinVar
10-59247701-A-C		not specified	Uncertain significance (Nov 22, 2021)
10-59251623-C-T		not specified	Uncertain significance (Apr 12, 2022)
10-59251653-C-T		not specified	Uncertain significance (Mar 20, 2023)
10-59252904-A-T		Malignant tumor of prostate	Uncertain significance (-)
10-59254368-G-A		not specified	Uncertain significance (Dec 06, 2021)
10-59254404-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-59262483-G-A		not specified	Uncertain significance (Apr 25, 2023)
10-59262493-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-59262507-T-C		not specified	Uncertain significance (Mar 22, 2023)
10-59262528-G-A		not specified	Likely benign (Jun 30, 2023)
10-59262534-G-A		not specified	Likely benign (Aug 13, 2021)
10-59262613-T-G		not specified	Uncertain significance (Jan 26, 2023)
10-59264100-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-59264160-G-A		not specified	Uncertain significance (Nov 08, 2021)
10-59264163-A-C		not specified	Uncertain significance (May 05, 2023)
10-59268633-G-C		not specified	Uncertain significance (May 05, 2023)
10-59268656-C-T		not specified	Uncertain significance (Dec 03, 2021)
10-59283390-C-T		not specified	Uncertain significance (Aug 22, 2022)
10-59302845-T-G		not specified	Uncertain significance (May 04, 2022)
10-59302860-C-G		not specified	Uncertain significance (Dec 19, 2022)
10-59352293-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-59352390-C-G		not specified	Uncertain significance (Feb 02, 2022)
10-59352401-G-A		not specified	Uncertain significance (Aug 12, 2021)
10-59352412-G-A		not specified	Uncertain significance (May 18, 2023)
10-59352437-C-A		not specified	Uncertain significance (Nov 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM13C	protein_coding	protein_coding	ENST00000373868	14	117050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000581	1.00	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	237	327	0.726	0.0000177	3856
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.000181	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000557	0.0000527
Middle Eastern	0.000181	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0774

Intolerance Scores

• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.75

Haploinsufficiency Scores

• pHI: 0.604
• hipred: Y
• hipred_score: 0.609
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.559

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam13c

Gene ontology

• Molecular function: protein binding