GHITM

protein-coding

growth hormone inducible transmembrane protein, the group of Transmembrane BAX inhibitor motif containing

Gene summary

Enables calcium:proton antiporter activity. Involved in calcium export from the mitochondrion; inner mitochondrial membrane organization; and negative regulation of release of cytochrome c from mitochondria. Located in endoplasmic reticulum membrane and mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014394.3

Inheritance

—

ClinVar variants

U:56B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr10:84,139,482-84,154,841

External References & Databases

Ensembl (ENSG00000165678)

Transcript & Mutation Effects

hg38 • Region Span ~15.4 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 GHITM variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014394.3. 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			51 clinvar	3 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	56	3	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014394.3	RefSeq	NP_055209.2	8	MANE Select
ENST00000372134.6	Ensembl	ENSP00000361207.3	8	MANE Select
ENST00000686247.1	Ensembl	ENSP00000509112.1	8	Standard
ENST00000686247.2	Ensembl	ENSP00000509112.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
biological_process

Molecular Function

molecular_function
protein binding

Cellular Component

mitochondrion
mitochondrial inner membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372134
Coding exons: 8
Length: 13806
Individuals with no LoFs: 124801
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 124846
p: 0.000180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0471	192	194	0.990	0.00000979	2201
Missense (PolyPhen)		40	48.735	0.82077		589
Synonymous	-0.227	69	66.6	1.04	0.00000333	719
Loss of Function	2.34	6	16.1	0.372	7.75e-7	205

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00027	0.00026	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00072	0.00072	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for the mitochondrial tubular network and cristae organization. Involved in apoptotic release of cytochrome c. {ECO:0000269|PubMed:18417609}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.594
RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.521

Gene Damage Prediction

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