TM9SF1

protein-coding

transmembrane 9 superfamily member 1, the group of Transmembrane 9 superfamily members

Gene summary

Predicted to be involved in protein localization to membrane. Predicted to be located in autophagosome membrane; cytoplasmic vesicle; and lysosomal membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006405.7

Inheritance

—

ClinVar variants

U:92

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr14:24,189,149-24,195,687

External References & Databases

Ensembl (ENSG00000100926)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 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 TM9SF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006405.7. 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			5 clinvar			5
missense			86 clinvar			86
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	92	0	0	92

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006405.7	RefSeq	NP_006396.2	5	MANE Select
ENST00000261789.9	Ensembl	ENSP00000261789.4	5	MANE Select
NM_001014842.3	RefSeq	NP_001014842.1	4	Standard
NM_001289006.2	RefSeq	NP_001275935.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

autophagy
protein localization to membrane

Cellular Component

autophagosome membrane
lysosomal membrane
membrane
integral component of membrane
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261789
Coding exons: 5
Length: 24331
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125748
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.11	255	369	0.691	0.0000225	3934
Missense (PolyPhen)		57	123.99	0.45971		1362
Synonymous	-0.100	144	142	1.01	0.00000801	1275
Loss of Function	1.96	15	25.8	0.582	0.00000159	242

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays an essential role in autophagy. {ECO:0000269|PubMed:19029833}.;

Recessive Scores

pRec: 0.134

Intolerance Scores

LoFtool: 0.651
RVIS EVS: 0.18
RVIS percentile EVS: 66.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.995

Gene Damage Prediction

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