HIGD1A

HIG1 hypoxia inducible domain family member 1A, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 3:42782908-42804490

Links

ENSG00000181061 ∙ NCBI:25994 ∙ OMIM:618623 ∙ HGNC:29527 ∙ Uniprot:Q9Y241 ∙ 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 HIGD1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIGD1A 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	11	0	0

Variants in HIGD1A

This is a list of pathogenic ClinVar variants found in the HIGD1A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-42785291-A-G		not specified	Uncertain significance (Apr 19, 2023)
3-42785293-A-C		not specified	Uncertain significance (Nov 07, 2022)
3-42785302-T-C		not specified	Uncertain significance (Dec 03, 2024)
3-42785312-A-G		not specified	Uncertain significance (Jan 10, 2023)
3-42786069-C-G		not specified	Uncertain significance (Aug 14, 2024)
3-42786118-G-C		not specified	Uncertain significance (Mar 31, 2024)
3-42786123-T-C		not specified	Uncertain significance (Mar 01, 2025)
3-42786127-A-C		not specified	Uncertain significance (Jun 09, 2022)
3-42794166-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-42794168-A-T		not specified	Uncertain significance (Nov 10, 2024)
3-42794189-C-T		not specified	Uncertain significance (Sep 02, 2024)
3-42804175-A-G		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIGD1A	protein_coding	protein_coding	ENST00000452906	4	47355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0327	0.831	124754	0	8	124762	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	59	62.3	0.947	0.00000324	683
Missense in Polyphen		10	10.912	0.91645		165
Synonymous	-0.251	21	19.6	1.07	0.00000107	203
Loss of Function	1.17	3	6.13	0.490	3.24e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000271	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed subunit of cytochrome c oxidase (COX, complex IV), which is the terminal component of the mitochondrial respiratory chain that catalyzes the reduction of oxygen to water. May play a role in the assembly of respiratory supercomplexes. {ECO:0000269|PubMed:22342701}.
• Pathway: Regulation of Hypoxia-inducible Factor (HIF) by oxygen (Consensus)

Recessive Scores

• pRec: 0.246

Intolerance Scores

• loftool: 0.485
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.172
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Higd1a

Gene ontology

• Biological process: cellular response to glucose starvation;negative regulation of apoptotic process;oxidation-reduction process;regulation of transcription from RNA polymerase II promoter in response to hypoxia;positive regulation of protein serine/threonine kinase activity;negative regulation of release of cytochrome c from mitochondria
• Cellular component: nucleoplasm;mitochondrion;mitochondrial inner membrane;integral component of membrane;protein-containing complex;respirasome