GHITM

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

Basic information

Region (hg38): 10:84139482-84154841

Links

ENSG00000165678NCBI:27069OMIM:619205HGNC:17281Uniprot:Q9H3K2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
2
clinvar
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)3099721
10-84141528-C-T not specified Uncertain significance (Dec 13, 2024)3853932
10-84141561-T-G not specified Uncertain significance (Dec 16, 2023)3099728
10-84141598-C-T not specified Uncertain significance (Jun 02, 2024)2354269
10-84142677-T-C not specified Uncertain significance (Jan 01, 2025)2390663
10-84142689-G-A not specified Uncertain significance (Dec 31, 2024)3099722
10-84142689-G-C not specified Uncertain significance (Jul 22, 2022)2302990
10-84142698-C-A not specified Uncertain significance (Mar 08, 2024)2409512
10-84142708-A-C not specified Uncertain significance (Jun 03, 2022)2216191
10-84143995-T-C not specified Uncertain significance (Apr 13, 2022)3099723
10-84144009-A-G not specified Uncertain significance (Oct 29, 2024)3520090
10-84144036-G-A not specified Uncertain significance (Feb 05, 2024)3099724
10-84144085-T-C not specified Uncertain significance (Mar 08, 2025)3853935
10-84144091-C-G not specified Uncertain significance (Mar 20, 2023)2527247
10-84144102-G-T not specified Uncertain significance (Apr 01, 2024)3281349
10-84144897-G-A not specified Uncertain significance (Sep 12, 2024)3520089
10-84144913-C-T not specified Uncertain significance (Dec 15, 2022)2335279
10-84144918-A-G not specified Uncertain significance (Sep 28, 2022)2406492
10-84144936-A-G not specified Likely benign (Jan 18, 2025)3853936
10-84144960-A-G not specified Uncertain significance (Jan 09, 2024)3099725
10-84144976-C-T not specified Uncertain significance (Sep 16, 2021)2356557
10-84144987-A-G not specified Uncertain significance (Aug 07, 2024)3520088
10-84144997-T-C not specified Uncertain significance (Feb 07, 2025)3853933
10-84145001-G-A not specified Uncertain significance (Sep 02, 2024)3520087
10-84148775-G-A not specified Uncertain significance (Apr 07, 2022)2228905

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GHITMprotein_codingprotein_codingENST00000372134 813806
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01150.9811248010451248460.000180
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.04711921940.9900.000009792201
Missense in Polyphen4048.7350.82077589
Synonymous-0.2276966.61.040.00000333719
Loss of Function2.34616.10.3727.75e-7205

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003230.000316
Ashkenazi Jewish0.000.00
East Asian0.0007230.000722
Finnish0.000.00
European (Non-Finnish)0.0001970.000194
Middle Eastern0.0007230.000722
South Asian0.0001310.000131
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ghitm
Phenotype

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