HEATR5A

protein-coding

HEAT repeat containing 5A, the group of Armadillo like helical domain containing

Gene summary

Predicted to be involved in endocytosis; intracellular protein localization; and retrograde transport, endosome to Golgi. Predicted to be located in cytosol. Predicted to be active in Golgi apparatus and endocytic vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C14orf125

MANE transcript

NM_015473.4

Inheritance

—

ClinVar variants

U:332B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr14:31,291,788-31,420,550

External References & Databases

Ensembl (ENSG00000129493)

Transcript & Mutation Effects

hg38 • Region Span ~128.8 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 HEATR5A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 317

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015473.4. 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			1 clinvar			1
missense			323 clinvar	8 clinvar		331
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	332	8	0	340

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015473.4	RefSeq	NP_056288.2	35	MANE Select
ENST00000543095.7	Ensembl	ENSP00000437968.2	35	MANE Select
ENST00000382464.6	Ensembl	ENSP00000371903.2	2	Standard
ENST00000382464.7	Ensembl	ENSP00000371903.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endocytosis
protein localization
retrograde transport, endosome to Golgi

Cellular Component

cytosol
endocytic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382464
Coding exons: 2
Length: 128795
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.504	45	55.6	0.810	0.00000282	738
Missense (PolyPhen)		18	25.347	0.71015		333
Synonymous	1.28	14	21.5	0.650	0.00000107	216
Loss of Function	0.736	2	3.48	0.574	1.45e-7	55

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.171

Gene Damage Prediction

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