TIMD4

protein-coding

T cell immunoglobulin and mucin domain containing 4, the group of V-set domain containing

Gene summary

Enables phosphatidylserine binding activity. Involved in apoptotic cell clearance. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_138379.3

Inheritance

—

ClinVar variants

U:47B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr5:156,919,292-156,963,226

External References & Databases

Ensembl (ENSG00000145850)

Transcript & Mutation Effects

hg38 • Region Span ~43.9 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 TIMD4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138379.3. 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						0
missense			42 clinvar	2 clinvar	4 clinvar	48
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	47	2	4	53

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138379.3	RefSeq	NP_612388.2	9	MANE Select
ENST00000274532.7	Ensembl	ENSP00000274532.2	9	MANE Select
NM_001146726.2	RefSeq	NP_001140198.1	8	Standard
ENST00000406964.5	Ensembl	ENSP00000385882.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ebola Virus Pathway on Host
Ebola Virus Pathway on Host

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000274532
Coding exons: 9
Length: 43974
Individuals with no LoFs: 125644
Homozygous LoFs: 0
Heterozygous LoFs: 104
Defined: 125748
p: 0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.363	234	219	1.07	0.0000123	2430
Missense (PolyPhen)		69	56.455	1.2222		663
Synonymous	-0.741	97	88.1	1.10	0.00000589	785
Loss of Function	0.476	16	18.2	0.880	8.58e-7	209

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.0013	0.0013	notable
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00033	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Phosphatidylserine receptor that enhances the engulfment of apoptotic cells. Involved in regulating T-cell proliferation and lymphotoxin signaling. Ligand for HAVCR1/TIMD1 (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0823

Intolerance Scores

LoFtool: 0.931
RVIS EVS: 0.16
RVIS percentile EVS: 64.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00107

Gene Damage Prediction

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