TM9SF3

protein-coding

transmembrane 9 superfamily member 3, the group of Transmembrane 9 superfamily members

Gene summary

Predicted to be involved in protein localization to membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020123.4

Inheritance

—

ClinVar variants

U:52

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr10:96,518,110-96,587,452

External References & Databases

Ensembl (ENSG00000077147)

Transcript & Mutation Effects

hg38 • Region Span ~69.3 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 TM9SF3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020123.4. 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			1 clinvar			1
missense			45 clinvar			45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	52	0	0	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020123.4	RefSeq	NP_064508.3	15	MANE Select
ENST00000371142.9	Ensembl	ENSP00000360184.4	15	MANE Select
ENST00000443638.1	Ensembl	ENSP00000401152.1	6	Standard
ENST00000852770.1	Ensembl	ENSP00000522829.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein localization to membrane

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371142
Coding exons: 15
Length: 69344
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.51	124	293	0.423	0.0000145	3835
Missense (PolyPhen)		25	105.57	0.23682		1322
Synonymous	0.348	90	94.3	0.954	0.00000467	1074
Loss of Function	5.32	0	33.0	0.00	0.00000169	434

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.0741
RVIS EVS: -0.41
RVIS percentile EVS: 26.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.268

Gene Damage Prediction

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