CLHC1

clathrin heavy chain linker domain containing 1, the group of TSNAXIP1 domain containing

Basic information

Region (hg38): 2:55172547-55232563

Previous symbols: [ "C2orf63" ]

Links

ENSG00000162994 ∙ NCBI:130162 ∙ ∙ HGNC:26453 ∙ Uniprot:Q8NHS4 ∙ 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 CLHC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLHC1 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			32	3		35
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	34	3	0

Variants in CLHC1

This is a list of pathogenic ClinVar variants found in the CLHC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-55175852-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-55175863-C-T		not specified	Uncertain significance (Dec 15, 2023)
2-55175875-G-A		not specified • EBV-positive nodal T- and NK-cell lymphoma	Likely benign (Jun 30, 2022)
2-55175913-A-C		not specified	Uncertain significance (Jan 24, 2024)
2-55175945-T-C		not specified	Uncertain significance (Dec 06, 2022)
2-55175980-A-G		not specified	Uncertain significance (Sep 26, 2023)
2-55177611-C-A		not specified	Uncertain significance (Sep 14, 2023)
2-55177640-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-55177697-G-T		not specified	Uncertain significance (Mar 21, 2024)
2-55177703-T-G		not specified	Likely benign (Sep 26, 2022)
2-55180557-G-C		not specified	Uncertain significance (Oct 18, 2021)
2-55180622-C-G		not specified	Uncertain significance (Feb 28, 2023)
2-55180663-G-C		not specified	Uncertain significance (Apr 04, 2024)
2-55180668-C-G		not specified	Uncertain significance (Dec 06, 2024)
2-55181584-C-G		not specified	Uncertain significance (Apr 17, 2024)
2-55181604-A-T		not specified	Uncertain significance (Jun 12, 2023)
2-55181606-C-T		Waddling gait;Marked Hypotonia	Likely pathogenic (Dec 01, 2014)
2-55181651-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-55181661-G-T		not specified	Uncertain significance (Nov 08, 2022)
2-55181663-C-A		not specified	Uncertain significance (Sep 16, 2021)
2-55181681-G-A		not specified	Uncertain significance (Oct 09, 2024)
2-55181690-A-C		not specified	Uncertain significance (Dec 02, 2022)
2-55181708-A-G		not specified	Uncertain significance (Jul 05, 2022)
2-55181744-G-C		not specified	Uncertain significance (Jun 13, 2022)
2-55206300-G-A			Uncertain significance (Sep 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLHC1	protein_coding	protein_coding	ENST00000401408	11	57773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.58e-21	0.00154	123237	18	2490	125745	0.0100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.949	341	295	1.16	0.0000137	3874
Missense in Polyphen		60	62.632	0.95798		865
Synonymous	-0.241	103	99.9	1.03	0.00000459	1045
Loss of Function	-0.0231	31	30.9	1.00	0.00000166	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00588	0.00588
Ashkenazi Jewish	0.0104	0.0104
East Asian	0.000326	0.000326
Finnish	0.0184	0.0185
European (Non-Finnish)	0.0124	0.0123
Middle Eastern	0.000326	0.000326
South Asian	0.0136	0.0133
Other	0.00970	0.00966

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.6

Haploinsufficiency Scores

• pHI: 0.0958
• hipred: N
• hipred_score: 0.123
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clhc1

Gene ontology

• Molecular function: protein binding