FAM13B

protein-coding

family with sequence similarity 13 member B, 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. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C5orf5
FAM13B1

MANE transcript

NM_001385994.1

Inheritance

—

ClinVar variants

U:118B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr5:137,937,960-138,051,961

External References & Databases

Ensembl (ENSG00000031003)

Transcript & Mutation Effects

hg38 • Region Span ~114.0 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 FAM13B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 110

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001385994.1. 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			2
missense			110 clinvar	1 clinvar		111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	118	1	0	119

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001385994.1	RefSeq	NP_001372923.1	22	MANE Select
ENST00000689681.1	Ensembl	ENSP00000509788.1	22	MANE Select
NM_001101800.3	RefSeq	NP_001095270.1	20	Standard
NM_001101801.3	RefSeq	NP_001095271.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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: ENST00000033079
Coding exons: 21
Length: 114002
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125741
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.861	414	466	0.888	0.0000231	6098
Missense (PolyPhen)		159	205.63	0.77322		2700
Synonymous	0.541	146	155	0.945	0.00000733	1604
Loss of Function	5.10	11	49.9	0.220	0.00000242	650

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000069	0.000065	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.477
RVIS EVS: -1
RVIS percentile EVS: 8.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.802

Gene Damage Prediction

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