HIGD1C

HIG1 hypoxia inducible domain family member 1C

Basic information

Region (hg38): 12:50952538-50970607

Links

ENSG00000214511 ∙ NCBI:613227 ∙ ∙ HGNC:28044 ∙ Uniprot:A8MV81 ∙ 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 HIGD1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIGD1C 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in HIGD1C

This is a list of pathogenic ClinVar variants found in the HIGD1C region.

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

Position	Type	Phenotype	Significance	ClinVar
12-50954051-G-A		not specified	Uncertain significance (Feb 23, 2023)
12-50954089-A-G		not specified	Likely benign (Mar 13, 2023)
12-50960977-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-50960991-G-C		not specified	Uncertain significance (May 18, 2023)
12-50961022-G-A		not specified	Uncertain significance (Jul 20, 2021)
12-50961057-A-T		not specified	Uncertain significance (Feb 04, 2025)
12-50961064-T-C		not specified	Uncertain significance (Apr 22, 2022)
12-50970444-G-A		not specified	Uncertain significance (Mar 22, 2023)
12-50970481-G-A		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIGD1C	protein_coding	protein_coding	ENST00000398455	3	16585

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000396	0.415	124435	1	199	124635	0.000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0270	46	46.5	0.989	0.00000209	615
Missense in Polyphen		17	14.829	1.1464		189
Synonymous	0.212	15	16.1	0.933	6.87e-7	186
Loss of Function	0.000305	5	5.00	1.00	2.97e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00818	0.00814
Ashkenazi Jewish	0.00	0.00
East Asian	0.00334	0.00334
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000354	0.0000354
Middle Eastern	0.00334	0.00334
South Asian	0.0000982	0.0000980
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.747
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Higd1c

Gene ontology

• Cellular component: integral component of membrane