ITM2A

integral membrane protein 2A, the group of BRICHOS domain containing

Basic information

Region (hg38): X:79360383-79367667

Links

ENSG00000078596 ∙ NCBI:9452 ∙ OMIM:300222 ∙ HGNC:6173 ∙ Uniprot:O43736 ∙ 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 ITM2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITM2A 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				1	1	2
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	1	2

Variants in ITM2A

This is a list of pathogenic ClinVar variants found in the ITM2A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-79361115-C-A		not specified	Uncertain significance (Jul 28, 2021)
X-79361339-G-T		not specified	Uncertain significance (Dec 17, 2023)
X-79361346-C-T		not specified	Uncertain significance (Feb 05, 2024)
X-79361416-G-A		not specified	Uncertain significance (Mar 06, 2023)
X-79361426-C-T			Benign (Dec 31, 2019)
X-79362586-G-C		not specified	Uncertain significance (Nov 13, 2023)
X-79362701-A-G			Benign (Dec 31, 2019)
X-79362959-T-A		not specified	Uncertain significance (Dec 02, 2022)
X-79363000-A-G		not specified	Uncertain significance (Aug 21, 2023)
X-79363001-C-A		not specified	Uncertain significance (Oct 05, 2023)
X-79363012-G-A		not specified	Uncertain significance (Mar 29, 2024)
X-79363028-C-T		not specified	Uncertain significance (Jul 22, 2022)
X-79363063-T-C		not specified	Uncertain significance (Apr 25, 2023)
X-79363078-C-T		not specified	Uncertain significance (May 16, 2024)
X-79363473-C-A		not specified	Uncertain significance (Sep 26, 2023)
X-79363537-G-C			Likely benign (Jan 01, 2023)
X-79363547-C-T		not specified	Uncertain significance (Jan 30, 2024)
X-79367193-G-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITM2A	protein_coding	protein_coding	ENST00000373298	6	7284

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.197	0.762	125698	1	4	125703	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	94	97.7	0.962	0.00000743	1718
Missense in Polyphen		9	20.943	0.42973		462
Synonymous	-0.935	39	32.2	1.21	0.00000213	519
Loss of Function	1.69	2	6.75	0.296	4.78e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000734	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000503	0.0000352
Middle Eastern	0.0000734	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.266
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.474
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itm2a
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; embryo phenotype

Gene ontology

• Biological process: plasma cell differentiation;immunoglobulin production;negative regulation of amyloid precursor protein biosynthetic process
• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane
• Molecular function: amyloid-beta binding;protein binding