TIMD4

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

Basic information

Region (hg38): 5:156919291-156963226

Links

ENSG00000145850 ∙ NCBI:91937 ∙ OMIM:610096 ∙ HGNC:25132 ∙ Uniprot:Q96H15 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TIMD4 gene.

• Inborn genetic diseases (13 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIMD4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			13		4	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	4

Variants in TIMD4

This is a list of pathogenic ClinVar variants found in the TIMD4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-156919501-C-T			Benign (Feb 26, 2018)
5-156920495-T-C		not specified	Uncertain significance (Feb 06, 2023)
5-156922114-C-A		not specified	Uncertain significance (Oct 02, 2023)
5-156922161-A-G		not specified	Uncertain significance (Jun 02, 2023)
5-156949654-T-G		not specified	Uncertain significance (Aug 31, 2023)
5-156951517-G-T		not specified	Uncertain significance (Jan 23, 2023)
5-156951574-G-A		not specified	Uncertain significance (Apr 28, 2023)
5-156951613-G-A		not specified	Uncertain significance (Nov 09, 2023)
5-156951635-T-C		not specified	Uncertain significance (May 08, 2023)
5-156951655-G-A			Benign (Aug 14, 2018)
5-156951677-C-T			Benign (Jun 29, 2018)
5-156951682-G-T			Benign (Aug 14, 2018)
5-156951718-C-T		not specified	Uncertain significance (Feb 23, 2023)
5-156951736-G-C		not specified	Uncertain significance (Apr 07, 2023)
5-156951751-C-T		not specified	Uncertain significance (Dec 15, 2023)
5-156951778-G-A		not specified	Uncertain significance (Aug 21, 2023)
5-156954433-G-T		not specified	Uncertain significance (Feb 07, 2023)
5-156954546-A-C		not specified	Uncertain significance (Mar 29, 2023)
5-156954598-C-T		not specified	Uncertain significance (Feb 27, 2024)
5-156954643-G-C		not specified	Uncertain significance (Oct 02, 2023)
5-156954646-C-G		not specified	Uncertain significance (Feb 03, 2022)
5-156954711-C-T		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TIMD4	protein_coding	protein_coding	ENST00000274532	9	43974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.64e-10	0.151	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.363	234	219	1.07	0.0000123	2430
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000705	0.000705
Ashkenazi Jewish	0.00139	0.00139
East Asian	0.00130	0.00131
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.00130	0.00131
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: Ebola Virus Pathway on Host;Ebola Virus Pathway on Host (Consensus)

Recessive Scores

• pRec: 0.0823

Intolerance Scores

• loftool: 0.931
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.82

Haploinsufficiency Scores

• pHI: 0.0633
• hipred: N
• hipred_score: 0.146
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Timd4
• Phenotype: immune system phenotype; hematopoietic system phenotype; cellular phenotype

Gene ontology

• Cellular component: integral component of membrane