HRCT1

histidine rich carboxyl terminus 1

Basic information

Region (hg38): 9:35906202-35907136

Links

ENSG00000196196 ∙ NCBI:646962 ∙ ∙ HGNC:33872 ∙ Uniprot:Q6UXD1 ∙ 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 HRCT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HRCT1 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			37	6		43
nonsense						0
start loss						0
frameshift						0
inframe indel				2		2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	8	0

Variants in HRCT1

This is a list of pathogenic ClinVar variants found in the HRCT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35906303-G-A		not specified	Uncertain significance (Jan 18, 2025)
9-35906315-C-G		not specified	Uncertain significance (Apr 14, 2023)
9-35906337-C-A		not specified	Uncertain significance (Jun 21, 2023)
9-35906339-G-C		not specified	Uncertain significance (Jan 04, 2024)
9-35906346-C-T		not specified	Uncertain significance (May 16, 2023)
9-35906375-A-G		not specified	Uncertain significance (Jul 14, 2021)
9-35906390-G-A		not specified	Likely benign (Oct 26, 2021)
9-35906393-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-35906394-G-A		not specified	Likely benign (Dec 17, 2023)
9-35906408-G-A		not specified	Uncertain significance (Oct 03, 2024)
9-35906415-G-C		not specified	Uncertain significance (Feb 26, 2024)
9-35906421-G-A		not specified	Uncertain significance (Sep 08, 2024)
9-35906436-G-A		not specified	Uncertain significance (Nov 03, 2022)
9-35906439-A-T		not specified	Uncertain significance (Dec 22, 2023)
9-35906442-G-A		not specified	Uncertain significance (Mar 10, 2025)
9-35906447-C-T		not specified	Uncertain significance (Jul 09, 2021)
9-35906448-G-A		not specified	Uncertain significance (Jul 14, 2024)
9-35906450-C-T		not specified	Likely benign (Apr 27, 2023)
9-35906451-G-A		not specified	Uncertain significance (May 09, 2023)
9-35906460-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-35906471-C-G		not specified	Uncertain significance (Jan 10, 2023)
9-35906475-G-A		not specified	Uncertain significance (Mar 14, 2025)
9-35906477-C-T		not specified	Uncertain significance (Dec 11, 2023)
9-35906478-G-A		not specified	Uncertain significance (Jun 07, 2023)
9-35906480-G-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HRCT1	protein_coding	protein_coding	ENST00000354323	1	950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.284	87	79.9	1.09	0.00000551	719
Missense in Polyphen		14	12.816	1.0924		151
Synonymous	-0.309	35	32.8	1.07	0.00000193	266
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.156
• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hrct1

Gene ontology

• Cellular component: integral component of membrane