CLHC1

protein-coding

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

Gene summary

Predicted to enable AP-1 adaptor complex binding activity and AP-3 adaptor complex binding activity. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C2orf63

MANE transcript

NM_152385.4

Inheritance

—

ClinVar variants

P:1U:103B:6

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 1

Max pathogenic AF

—

Genomic locus

chr2:55,172,547-55,232,563

External References & Databases

Ensembl (ENSG00000162994)

Transcript & Mutation Effects

hg38 • Region Span ~60.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLHC1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 99

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

Waddling gaitTotal: 1

Marked HypotoniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152385.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense		1 clinvar	97 clinvar	6 clinvar		104
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	103	6	0	110

Highest pathogenic variant AF is 0.00028345725

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152385.4	RefSeq	NP_689598.2	11	MANE Select
ENST00000401408.6	Ensembl	ENSP00000384869.1	11	MANE Select
NM_001135598.2	RefSeq	NP_001129070.1	9	Standard
NM_001353779.2	RefSeq	NP_001340708.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401408
Coding exons: 11
Length: 57773
Individuals with no LoFs: 123237
Homozygous LoFs: 18
Heterozygous LoFs: 2490
Defined: 125745
p: 0.0100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.949	341	295	1.16	0.0000137	3874
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0028	0.0028	notable
Latino/Admixed American	0.0031	0.0031	notable
Ashkenazi Jewish	0.010	0.010	notable
East Asian	0.00033	0.00033	rare
Finnish	0.018	0.018	notable
European (Non-Finnish)	0.012	0.012	notable
South Asian	0.014	0.013	notable
Other	0.0097	0.0097	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.16
RVIS percentile EVS: 92.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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