HDHD5

haloacid dehalogenase like hydrolase domain containing 5, the group of Haloacid dehalogenase like hydrolase domain containing

Basic information

Region (hg38): 22:17137511-17165287

Previous symbols: [ "CECR5" ]

Links

ENSG00000069998 ∙ NCBI:27440 ∙ ∙ HGNC:1843 ∙ Uniprot:Q9BXW7 ∙ 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 HDHD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDHD5 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				1		1
missense			49	6	2	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	7	2

Variants in HDHD5

This is a list of pathogenic ClinVar variants found in the HDHD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-17138047-G-A			Likely benign (Aug 08, 2018)
22-17138056-G-C		not specified	Uncertain significance (Sep 06, 2022)
22-17138074-C-T		not specified	Uncertain significance (Aug 10, 2023)
22-17138086-C-A		not specified	Uncertain significance (Apr 23, 2024)
22-17138091-G-A		not specified	Uncertain significance (Dec 27, 2022)
22-17138112-C-T		not specified	Uncertain significance (Nov 10, 2024)
22-17138133-C-T		not specified	Uncertain significance (Apr 18, 2023)
22-17138143-G-C		not specified	Uncertain significance (Jun 07, 2024)
22-17138172-G-A		not specified	Uncertain significance (Oct 23, 2024)
22-17138186-C-G			Benign (Dec 31, 2019)
22-17138191-G-T		not specified	Uncertain significance (Jul 14, 2021)
22-17138266-C-T		not specified	Uncertain significance (Jul 13, 2021)
22-17138271-C-T		not specified	Uncertain significance (Nov 09, 2024)
22-17138325-T-G		not specified	Uncertain significance (Oct 30, 2023)
22-17138338-C-T		not specified	Likely benign (Feb 16, 2023)
22-17138559-T-C		not specified	Uncertain significance (May 17, 2023)
22-17138587-C-T		not specified	Uncertain significance (Jan 02, 2024)
22-17138627-C-A		not specified	Uncertain significance (Aug 12, 2024)
22-17138627-C-G		not specified	Uncertain significance (Dec 07, 2023)
22-17138644-T-C		not specified	Uncertain significance (Dec 10, 2024)
22-17138652-C-T		not specified	Uncertain significance (Aug 14, 2024)
22-17138677-C-G		not specified	Uncertain significance (May 11, 2022)
22-17138724-G-A		not specified	Uncertain significance (Sep 22, 2023)
22-17141064-C-A		not specified	Uncertain significance (Nov 26, 2024)
22-17141111-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDHD5	protein_coding	protein_coding	ENST00000336737	8	27777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-9	0.192	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.183	233	241	0.967	0.0000146	2689
Missense in Polyphen		52	60.726	0.85631		644
Synonymous	-0.228	110	107	1.03	0.00000693	898
Loss of Function	0.513	15	17.3	0.867	9.96e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000577	0.000577
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000272	0.000272
South Asian	0.000264	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.123
• ghis: 0.515

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hdhd5