FAM91A1

protein-coding

family with sequence similarity 91 member A1

Gene summary

Involved in intracellular protein transport and vesicle tethering to Golgi. Located in cytoplasmic vesicle and trans-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_144963.4

Inheritance

—

ClinVar variants

U:99B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr8:123,768,439-123,815,452

External References & Databases

Ensembl (ENSG00000176853)

Transcript & Mutation Effects

hg38 • Region Span ~47.0 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 FAM91A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144963.4. 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			2
missense			88 clinvar	4 clinvar	1 clinvar	93
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	99	4	1	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144963.4	RefSeq	NP_659400.3	24	MANE Select
ENST00000334705.12	Ensembl	ENSP00000335082.7	24	MANE Select
NM_001317917.2	RefSeq	NP_001304846.2	16	Standard
NM_001317918.1	RefSeq	NP_001304847.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gastric Cancer Network 2

Biological Process

intracellular protein transport
vesicle tethering to Golgi

Molecular Function

protein binding

Cellular Component

trans-Golgi network
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334705
Coding exons: 24
Length: 46997
Individuals with no LoFs: 124766
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 124793
p: 0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.16	312	440	0.710	0.0000221	5471
Missense (PolyPhen)		56	136.11	0.41143		1742
Synonymous	1.33	135	156	0.864	0.00000784	1600
Loss of Function	4.44	16	49.8	0.321	0.00000259	616

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: As component of the WDR11 complex acts together with TBC1D23 to facilitate the golgin-mediated capture of vesicles generated using AP-1. {ECO:0000269|PubMed:29426865}.;

Intolerance Scores

RVIS EVS: -0.62
RVIS percentile EVS: 17.31

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.506

Gene Damage Prediction

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