HHATL

hedgehog acyltransferase like, the group of Membrane bound O-acyltransferase family

Basic information

Region (hg38): 3:42692663-42702824

Previous symbols: [ "C3orf3", "GUP1" ]

Links

ENSG00000010282 ∙ NCBI:57467 ∙ OMIM:608116 ∙ HGNC:13242 ∙ Uniprot:Q9HCP6 ∙ 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 HHATL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HHATL 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			42	1		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	1	0

Variants in HHATL

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

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

Position	Type	Phenotype	Significance	ClinVar
3-42692789-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-42692809-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-42692827-A-G		not specified	Uncertain significance (Sep 30, 2024)
3-42692851-A-G		not specified	Uncertain significance (Mar 01, 2024)
3-42692854-G-A		not specified	Uncertain significance (May 14, 2024)
3-42692860-G-A		not specified	Uncertain significance (May 23, 2023)
3-42693094-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-42693193-C-T		not specified	Uncertain significance (Dec 11, 2024)
3-42693217-G-A		not specified	Uncertain significance (Apr 17, 2024)
3-42693625-G-A		HHATL-related disorder	Uncertain significance (Mar 29, 2023)
3-42693712-T-C		not specified	Uncertain significance (Jun 28, 2024)
3-42693715-C-A		not specified	Uncertain significance (Sep 04, 2024)
3-42693798-C-A		not specified	Uncertain significance (Dec 11, 2024)
3-42693810-T-G		not specified	Uncertain significance (Sep 08, 2024)
3-42693818-T-G		not specified	Uncertain significance (Dec 17, 2024)
3-42696866-C-T		not specified	Uncertain significance (Aug 30, 2022)
3-42697023-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-42697062-C-T		not specified	Uncertain significance (Mar 09, 2025)
3-42697066-G-C		not specified	Uncertain significance (Jan 26, 2022)
3-42697098-C-T		not specified	Uncertain significance (Mar 28, 2023)
3-42697143-C-A		not specified	Uncertain significance (Feb 05, 2024)
3-42697528-C-T		not specified	Uncertain significance (Oct 16, 2023)
3-42697630-C-T		not specified	Uncertain significance (Jan 01, 2025)
3-42697654-C-T		not specified	Uncertain significance (Oct 07, 2024)
3-42697664-G-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HHATL	protein_coding	protein_coding	ENST00000441594	11	10165

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-7	0.964	125684	0	61	125745	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.556	275	302	0.910	0.0000178	3239
Missense in Polyphen		106	117.73	0.90038		1317
Synonymous	1.29	104	122	0.852	0.00000711	1031
Loss of Function	2.01	15	26.1	0.575	0.00000145	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000801	0.000801
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000575	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.0000575	0.0000544
South Asian	0.000458	0.000457
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates N-terminal palmitoylation of SHH by HHAT/SKN. {ECO:0000250}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.577
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.333
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hhatl

Gene ontology

• Biological process: negative regulation of N-terminal protein palmitoylation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;perinuclear region of cytoplasm