FAM13A

family with sequence similarity 13 member A, the group of Rho GTPase activating proteins

Basic information

Region (hg38): 4:88725954-89111398

Previous symbols: [ "FAM13A1" ]

Links

ENSG00000138640 ∙ NCBI:10144 ∙ OMIM:613299 ∙ HGNC:19367 ∙ Uniprot:O94988 ∙ 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 FAM13A gene.

• Inborn genetic diseases (36 variants)
• not provided (9 variants)
• Squamous cell carcinoma (1 variants)
• Chronic obstructive pulmonary disease (1 variants)
• Lung adenocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM13A 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					2	2
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			3	1	3	7
Total	0	0	36	2	5

Variants in FAM13A

This is a list of pathogenic ClinVar variants found in the FAM13A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-88731430-T-TA			Benign (Feb 26, 2018)
4-88732054-G-A		not specified	Uncertain significance (Mar 06, 2023)
4-88732091-G-A			Benign (Aug 22, 2018)
4-88732129-A-T		not specified	Uncertain significance (Mar 24, 2023)
4-88739101-T-G		not specified	Uncertain significance (Jun 22, 2021)
4-88746933-G-A		Squamous cell carcinoma • not specified	Conflicting classifications of pathogenicity (Jun 06, 2022)
4-88746982-C-T		not specified	Uncertain significance (Dec 02, 2021)
4-88746985-T-C		not specified	Uncertain significance (Jan 16, 2024)
4-88747647-C-T			Likely benign (Apr 03, 2018)
4-88747653-C-T		not specified	Uncertain significance (Dec 17, 2021)
4-88747662-C-T		not specified	Uncertain significance (Aug 17, 2022)
4-88747665-T-A		not specified	Uncertain significance (Dec 20, 2023)
4-88747762-C-G		not specified	Uncertain significance (Dec 22, 2023)
4-88749009-T-G		not specified	Uncertain significance (Jun 11, 2021)
4-88749811-C-T		not specified	Uncertain significance (Nov 18, 2022)
4-88749812-G-A		not specified	Uncertain significance (Oct 27, 2021)
4-88749844-G-C		not specified	Uncertain significance (Jan 09, 2024)
4-88749883-T-C		not specified	Uncertain significance (Jan 04, 2022)
4-88750451-G-A		not specified	Uncertain significance (Sep 09, 2021)
4-88750500-C-T		not specified	Uncertain significance (Oct 06, 2021)
4-88750527-C-T		not specified	Uncertain significance (Jul 27, 2021)
4-88750550-C-T		not specified	Uncertain significance (Jan 06, 2023)
4-88750589-T-A		not specified	Uncertain significance (Nov 07, 2022)
4-88750594-G-C		not specified	Uncertain significance (Aug 20, 2023)
4-88750607-C-G		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM13A	protein_coding	protein_coding	ENST00000264344	24	385444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.90e-18	0.978	125132	2	614	125748	0.00245

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.801	510	563	0.905	0.0000311	6758
Missense in Polyphen		164	200.42	0.81828		2377
Synonymous	1.13	190	211	0.901	0.0000117	1904
Loss of Function	2.64	38	60.1	0.633	0.00000345	683

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00382	0.00367
Ashkenazi Jewish	0.00199	0.00189
East Asian	0.000116	0.000109
Finnish	0.0141	0.0141
European (Non-Finnish)	0.00141	0.00133
Middle Eastern	0.000116	0.000109
South Asian	0.000673	0.000621
Other	0.00341	0.00326

dbNSFP

Source: dbNSFP

• Pathway: Lung fibrosis;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.987
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.26

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.306
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam13a
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol
• Molecular function: GTPase activator activity