FAM13A

protein-coding

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

Gene summary

Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM13A1

MANE transcript

NM_014883.4

Inheritance

—

ClinVar variants

P:1U:132B:11

Top phenotype

Squamous cell carcinoma

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr4:88,725,955-89,111,398

External References & Databases

Ensembl (ENSG00000138640)

Transcript & Mutation Effects

hg38 • Region Span ~385.4 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 FAM13A variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 125

not providedTotal: 10

Squamous cell carcinomaTotal: 1

FAM13A-related pulmonary fibrosisTotal: 1

Lung adenocarcinomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014883.4. 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			2 clinvar	3 clinvar	2 clinvar	7
missense		1 clinvar	126 clinvar	5 clinvar	1 clinvar	133
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	132	8	3	144

Highest pathogenic variant AF is 0.000047311874

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014883.4	RefSeq	NP_055698.2	24	MANE Select
ENST00000264344.10	Ensembl	ENSP00000264344.5	24	MANE Select
NM_001015045.3	RefSeq	NP_001015045.1	18	Standard
NM_001265578.2	RefSeq	NP_001252507.1	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lung fibrosis
Signal Transduction
Rho GTPase cycle
Signaling by Rho GTPases

Biological Process

signal transduction
positive regulation of GTPase activity
regulation of small GTPase mediated signal transduction

Molecular Function

GTPase activator activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264344
Coding exons: 24
Length: 385444
Individuals with no LoFs: 125132
Homozygous LoFs: 2
Heterozygous LoFs: 614
Defined: 125748
p: 0.00245

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.801	510	563	0.905	0.0000311	6758
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0012	notable
Latino/Admixed American	0.0024	0.0023	notable
Ashkenazi Jewish	0.0020	0.0019	notable
East Asian	0.00012	0.00011	rare
Finnish	0.014	0.014	notable
European (Non-Finnish)	0.0014	0.0013	notable
South Asian	0.00067	0.00062	rare
Other	0.0034	0.0033	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.987
RVIS EVS: -0.37
RVIS percentile EVS: 28.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.302

Gene Damage Prediction

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