DTHD1

death domain containing 1

Basic information

Region (hg38): 4:36281615-36347511

Links

ENSG00000197057 ∙ NCBI:401124 ∙ OMIM:616979 ∙ HGNC:37261 ∙ Uniprot:Q6ZMT9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• LCAT deficiency (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DTHD1 gene.

• not provided (379 variants)
• Inborn genetic diseases (37 variants)
• Retinal dystrophy (2 variants)
• Muscular dystrophy;Leber congenital amaurosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTHD1 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			4	64	5	73
missense			228	6	10	244
nonsense			9	1		10
start loss						0
frameshift			9			9
inframe indel			3			3
splice donor/acceptor (+/-2bp)			4			4
splice region			8	9		17
non coding			4	22	6	32
Total	0	0	261	93	21

Variants in DTHD1

This is a list of pathogenic ClinVar variants found in the DTHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-36282014-T-C		Muscular dystrophy;Leber congenital amaurosis	Uncertain significance (Jan 04, 2024)
4-36282015-G-A			Uncertain significance (Sep 06, 2022)
4-36282021-C-T		DTHD1-related disorder	Likely benign (Aug 07, 2023)
4-36282022-G-A			Uncertain significance (Aug 09, 2022)
4-36282026-A-C			Uncertain significance (Mar 01, 2022)
4-36282031-C-G			Uncertain significance (Nov 22, 2021)
4-36282039-CT-C			Benign (Jul 12, 2023)
4-36282039-C-CT			Benign (Jan 19, 2024)
4-36282047-T-C			Likely benign (Mar 29, 2021)
4-36282049-G-C			Likely benign (Mar 28, 2022)
4-36282049-G-T			Likely benign (Jul 10, 2023)
4-36284096-C-T		not specified	Uncertain significance (Dec 13, 2023)
4-36284129-C-G		not specified	Uncertain significance (Oct 21, 2021)
4-36284172-A-G		not specified	Uncertain significance (Apr 07, 2023)
4-36284195-C-A		not specified	Uncertain significance (Oct 17, 2023)
4-36284205-G-A		DTHD1-related disorder	Likely benign (Apr 16, 2019)
4-36284224-C-A		not specified	Uncertain significance (Feb 23, 2023)
4-36284291-C-T		not specified	Uncertain significance (Feb 05, 2024)
4-36284302-C-T		not specified	Likely benign (Sep 20, 2023)
4-36284312-G-T		not specified	Uncertain significance (Dec 14, 2023)
4-36284342-C-T		not specified	Uncertain significance (Jul 19, 2023)
4-36284383-A-G		not specified	Uncertain significance (Nov 08, 2022)
4-36284428-A-G		not specified	Uncertain significance (Jan 17, 2024)
4-36290357-C-A			Likely benign (May 20, 2023)
4-36290365-C-T			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTHD1	protein_coding	protein_coding	ENST00000456874	9	64135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.40e-7	0.986	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.989	332	387	0.859	0.0000189	5133
Missense in Polyphen		62	78.601	0.78879		1100
Synonymous	2.52	100	138	0.726	0.00000693	1473
Loss of Function	2.26	15	27.9	0.538	0.00000131	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.59
• rvis_percentile_EVS: 95.84

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dthd1

Gene ontology

• Biological process: signal transduction