HHLA1

HERV-H LTR-associating 1

Basic information

Region (hg38): 8:132061480-132111159

Previous symbols: [ "PLA2L" ]

Links

ENSG00000132297 ∙ NCBI:10086 ∙ OMIM:604109 ∙ HGNC:4904 ∙ Uniprot:C9JL84 ∙ 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 HHLA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HHLA1 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			31	4		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	5	0

Variants in HHLA1

This is a list of pathogenic ClinVar variants found in the HHLA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-132065903-C-A		not specified	Uncertain significance (Sep 30, 2021)
8-132071346-T-C		not specified	Uncertain significance (Sep 17, 2021)
8-132071382-C-T		not specified	Uncertain significance (Dec 18, 2023)
8-132071449-G-A		not specified	Uncertain significance (May 13, 2024)
8-132071457-G-A		not specified	Uncertain significance (Apr 25, 2023)
8-132071471-C-A		not specified	Uncertain significance (Jul 13, 2021)
8-132076079-C-T		not specified	Uncertain significance (Jun 24, 2022)
8-132076091-C-T		not specified	Uncertain significance (Oct 06, 2024)
8-132076096-C-G		not specified	Uncertain significance (Jun 04, 2024)
8-132076100-C-A		not specified	Uncertain significance (Mar 05, 2024)
8-132076124-G-A		not specified	Uncertain significance (May 16, 2022)
8-132077776-G-A		not specified	Uncertain significance (Nov 22, 2024)
8-132077810-C-T		not specified	Uncertain significance (Oct 26, 2022)
8-132077817-G-A			Likely benign (Apr 01, 2023)
8-132077845-C-T		not specified	Uncertain significance (Oct 17, 2024)
8-132077860-G-C		not specified	Uncertain significance (Jun 05, 2024)
8-132077903-C-A		not specified	Uncertain significance (Aug 09, 2021)
8-132077903-C-T		not specified	Likely benign (Jul 20, 2021)
8-132077908-G-A		not specified	Likely benign (Feb 28, 2023)
8-132077923-G-A		not specified	Uncertain significance (Mar 31, 2024)
8-132079730-G-C		not specified	Uncertain significance (May 31, 2022)
8-132079763-C-A		not specified	Uncertain significance (Feb 03, 2022)
8-132079771-G-A		not specified	Uncertain significance (May 29, 2024)
8-132079819-G-A		not specified	Uncertain significance (Sep 02, 2024)
8-132079889-C-T		not specified	Likely benign (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HHLA1	protein_coding	protein_coding	ENST00000434736	16	49674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.91e-14	0.0716	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	247	280	0.881	0.0000139	3488
Missense in Polyphen		57	72.565	0.78551		994
Synonymous	0.686	95	104	0.914	0.00000560	1075
Loss of Function	0.659	23	26.7	0.862	0.00000113	353

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

Haploinsufficiency Scores

• pHI: 0.0490

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hhla1

Gene ontology

• Cellular component: extracellular region