TMEM31

transmembrane protein 31

Basic information

Region (hg38): X:103710908-103714032

Links

ENSG00000179363 ∙ NCBI:203562 ∙ OMIM:301102 ∙ HGNC:28601 ∙ Uniprot:Q5JXX7 ∙ 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 TMEM31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM31 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			7	1		8
nonsense			1	1		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	8	3	0

Variants in TMEM31

This is a list of pathogenic ClinVar variants found in the TMEM31 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-103713526-T-C			Likely benign (Feb 25, 2018)
X-103713612-C-T			Uncertain significance (Mar 01, 2019)
X-103713616-C-T		not specified	Uncertain significance (Mar 04, 2024)
X-103713618-C-A		not specified	Uncertain significance (Mar 04, 2024)
X-103713633-C-A		not specified	Uncertain significance (Apr 25, 2023)
X-103713648-C-T			Likely benign (Dec 31, 2019)
X-103713649-G-T		not specified	Uncertain significance (Jun 17, 2022)
X-103713661-G-A		not specified	Likely benign (May 15, 2023)
X-103713691-C-G		not specified	Uncertain significance (Dec 15, 2023)
X-103713698-C-A		not specified	Uncertain significance (Jun 17, 2024)
X-103713715-C-T		not specified	Uncertain significance (Sep 17, 2021)
X-103713741-C-T		not specified	Uncertain significance (Apr 08, 2024)
X-103713802-C-A			Likely benign (-)
X-103713849-G-A		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM31	protein_coding	protein_coding	ENST00000319560	2	3120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00129	0.428	125715	10	17	125742	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.273	54	59.9	0.901	0.00000452	1097
Missense in Polyphen		15	15.506	0.96737		206
Synonymous	0.501	20	23.1	0.867	0.00000179	340
Loss of Function	-0.163	4	3.66	1.09	3.62e-7	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00254	0.00189
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000976	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.67

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• 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

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding