CLUH

protein-coding

clustered mitochondria homolog, the group of MicroRNA protein coding host genes

Gene summary

Enables mRNA binding activity. Involved in intracellular distribution of mitochondria and mitochondrion organization. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA0664

MANE transcript

NM_001366661.1

Inheritance

—

ClinVar variants

U:221B:13

Top phenotype

Hirschsprung disease, susceptibility to, 1

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr17:2,689,386-2,712,663

External References & Databases

Ensembl (ENSG00000132361)

Transcript & Mutation Effects

hg38 • Region Span ~23.3 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 CLUH variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 207

not providedTotal: 14

Hirschsprung disease, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366661.1. 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			2 clinvar	5 clinvar	3 clinvar	10
missense			211 clinvar	5 clinvar		216
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	221	10	3	234

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366661.1	RefSeq	NP_001353590.1	26	MANE Select
ENST00000651024.2	Ensembl	ENSP00000498679.1	26	MANE Select
NM_001366662.1	RefSeq	NP_001353591.1	25	Standard
NM_015229.4	RefSeq	NP_056044.4	26	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Translation Factors

Biological Process

mitochondrion organization
intracellular distribution of mitochondria

Molecular Function

mRNA binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000570628
Coding exons: 25
Length: 23278
Individuals with no LoFs: 124594
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 124620
p: 0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.84	698	849	0.822	0.0000589	8412
Missense (PolyPhen)		148	295.12	0.50149		2751
Synonymous	-3.86	494	396	1.25	0.0000325	2565
Loss of Function	5.96	10	59.7	0.168	0.00000318	652

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00059	0.00032	rare
Latino/Admixed American	0.00012	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000062	0.000056	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: mRNA-binding protein involved in proper cytoplasmic distribution of mitochondria. Specifically binds mRNAs of nuclear- encoded mitochondrial proteins in the cytoplasm and regulates transport or translation of these transcripts close to mitochondria, playing a role in mitochondrial biogenesis. {ECO:0000255|HAMAP-Rule:MF_03013, ECO:0000269|PubMed:25349259}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

RVIS EVS: -2.23
RVIS percentile EVS: 1.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N

Gene Damage Prediction

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