DTHD1

death domain containing 1

Basic information

Region (hg38): 4:36281616-36347511

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 (445 variants)
• not_specified (110 variants)
• DTHD1-related_disorder (10 variants)
• Retinal_dystrophy (6 variants)
• Leber_congenital_amaurosis (1 variants)
• LCAT_deficiency (1 variants)
• Optic_atrophy (1 variants)
• Muscular_dystrophy (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. These statistics are base on transcript: NM_001170700.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	75	3	82
missense			306	14	4	324
nonsense			9	1		10
start loss						0
frameshift			14	1		15
splice donor/acceptor (+/-2bp)			4	1		5
Total	0	0	337	92	7

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