TMEM41A

transmembrane protein 41A

Basic information

Region (hg38): 3:185476496-185499057

Links

ENSG00000163900 ∙ NCBI:90407 ∙ ∙ HGNC:30544 ∙ Uniprot:Q96HV5 ∙ 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 TMEM41A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM41A 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in TMEM41A

This is a list of pathogenic ClinVar variants found in the TMEM41A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-185480243-G-A		not specified	Uncertain significance (Apr 15, 2024)
3-185480246-T-C		not specified	Uncertain significance (Jan 30, 2024)
3-185480324-A-G		not specified	Uncertain significance (May 16, 2022)
3-185480368-C-T		not specified	Uncertain significance (Oct 12, 2021)
3-185480377-G-A		not specified	Uncertain significance (May 04, 2023)
3-185480404-A-G		not specified	Uncertain significance (Mar 29, 2024)
3-185480473-C-T		not specified	Uncertain significance (May 09, 2024)
3-185482377-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-185482394-G-C		not specified	Uncertain significance (Dec 27, 2023)
3-185491580-T-G		not specified	Uncertain significance (Feb 27, 2024)
3-185491595-T-G		not specified	Uncertain significance (Jan 29, 2024)
3-185491743-T-G		not specified	Uncertain significance (Sep 13, 2023)
3-185494629-G-T		not specified	Uncertain significance (Mar 15, 2024)
3-185494761-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-185495251-G-A		not specified	Uncertain significance (May 31, 2023)
3-185496838-G-A		not specified	Uncertain significance (Jul 15, 2021)
3-185496962-C-T		not specified	Uncertain significance (Dec 08, 2023)
3-185498937-G-C		not specified	Uncertain significance (Mar 28, 2024)
3-185498954-G-A		not specified	Uncertain significance (Dec 20, 2021)
3-185498955-G-A		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM41A	protein_coding	protein_coding	ENST00000421852	5	22562

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000293	0.811	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.464	120	135	0.888	0.00000696	1655
Missense in Polyphen		33	35.447	0.93097		495
Synonymous	-0.681	70	63.1	1.11	0.00000345	551
Loss of Function	1.17	7	11.2	0.624	5.42e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000212	0.000211
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000498	0.0000462
European (Non-Finnish)	0.000187	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000172	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.352
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.35

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.292
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem41a
• Phenotype: normal phenotype

Gene ontology

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