GHITM

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

Basic information

Region (hg38): 10:84139482-84154841

Links

ENSG00000165678 ∙ NCBI:27069 ∙ OMIM:619205 ∙ HGNC:17281 ∙ Uniprot:Q9H3K2 ∙ 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 GHITM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GHITM 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in GHITM

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

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

Position	Type	Phenotype	Significance	ClinVar
10-84141514-G-A		not specified	Uncertain significance (Feb 02, 2024)
10-84141528-C-T		not specified	Uncertain significance (Dec 13, 2024)
10-84141561-T-G		not specified	Uncertain significance (Dec 16, 2023)
10-84141598-C-T		not specified	Uncertain significance (Jun 02, 2024)
10-84142677-T-C		not specified	Uncertain significance (Jan 01, 2025)
10-84142689-G-A		not specified	Uncertain significance (Dec 31, 2024)
10-84142689-G-C		not specified	Uncertain significance (Jul 22, 2022)
10-84142698-C-A		not specified	Uncertain significance (Mar 08, 2024)
10-84142708-A-C		not specified	Uncertain significance (Jun 03, 2022)
10-84143995-T-C		not specified	Uncertain significance (Apr 13, 2022)
10-84144009-A-G		not specified	Uncertain significance (Oct 29, 2024)
10-84144036-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-84144085-T-C		not specified	Uncertain significance (Mar 08, 2025)
10-84144091-C-G		not specified	Uncertain significance (Mar 20, 2023)
10-84144102-G-T		not specified	Uncertain significance (Apr 01, 2024)
10-84144897-G-A		not specified	Uncertain significance (Sep 12, 2024)
10-84144913-C-T		not specified	Uncertain significance (Dec 15, 2022)
10-84144918-A-G		not specified	Uncertain significance (Sep 28, 2022)
10-84144936-A-G		not specified	Likely benign (Jan 18, 2025)
10-84144960-A-G		not specified	Uncertain significance (Jan 09, 2024)
10-84144976-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-84144987-A-G		not specified	Uncertain significance (Aug 07, 2024)
10-84144997-T-C		not specified	Uncertain significance (Feb 07, 2025)
10-84145001-G-A		not specified	Uncertain significance (Sep 02, 2024)
10-84148775-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GHITM	protein_coding	protein_coding	ENST00000372134	8	13806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0115	0.981	124801	0	45	124846	0.000180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0471	192	194	0.990	0.00000979	2201
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000323	0.000316
Ashkenazi Jewish	0.00	0.00
East Asian	0.000723	0.000722
Finnish	0.00	0.00
European (Non-Finnish)	0.000197	0.000194
Middle Eastern	0.000723	0.000722
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.465
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.521

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ghitm

Gene ontology

• Biological process: apoptotic process;biological_process
• Cellular component: mitochondrion;mitochondrial inner membrane;integral component of membrane;extracellular exosome
• Molecular function: molecular_function;protein binding