TMEM131L

transmembrane 131 like

Basic information

Region (hg38): 4:153466345-153636711

Previous symbols: [ "KIAA0922" ]

Links

ENSG00000121210 ∙ NCBI:23240 ∙ OMIM:616243 ∙ HGNC:29146 ∙ Uniprot:A2VDJ0 ∙ 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 TMEM131L gene.

• Inborn genetic diseases (31 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMEM131L 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				2	1	3
missense			30	1	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	3	2

Variants in TMEM131L

This is a list of pathogenic ClinVar variants found in the TMEM131L region.

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

Position	Type	Phenotype	Significance	ClinVar
4-153466405-G-T		not specified	Uncertain significance (Jul 20, 2021)
4-153466414-G-A		not specified	Uncertain significance (Apr 14, 2023)
4-153466414-G-T		not specified	Uncertain significance (Feb 27, 2024)
4-153466416-C-T		not specified	Uncertain significance (Dec 17, 2021)
4-153466441-C-G		not specified	Uncertain significance (Dec 16, 2021)
4-153466485-C-G		not specified	Uncertain significance (Mar 04, 2024)
4-153467211-C-T		not specified	Uncertain significance (Feb 10, 2023)
4-153550091-T-G		not specified	Uncertain significance (Apr 28, 2022)
4-153555834-G-A		not specified	Uncertain significance (Mar 05, 2024)
4-153555894-C-T		not specified	Uncertain significance (Dec 08, 2023)
4-153558277-G-A		not specified	Uncertain significance (Jul 14, 2023)
4-153558281-A-C		not specified	Uncertain significance (Jun 22, 2023)
4-153558286-C-T		not specified	Uncertain significance (Mar 01, 2023)
4-153558328-T-C		not specified	Uncertain significance (Jul 14, 2021)
4-153580861-A-C		not specified	Uncertain significance (Oct 05, 2022)
4-153581540-C-T		not specified	Uncertain significance (Feb 03, 2022)
4-153583586-G-C		not specified	Uncertain significance (Mar 24, 2023)
4-153583670-A-G		not specified	Likely benign (Nov 21, 2022)
4-153584835-C-T		not specified	Uncertain significance (Nov 29, 2023)
4-153585489-T-G		not specified	Uncertain significance (Oct 14, 2023)
4-153585514-C-G		not specified	Uncertain significance (Nov 22, 2023)
4-153585582-C-T		not specified	Uncertain significance (Jun 30, 2022)
4-153586227-C-T		not specified	Uncertain significance (Mar 08, 2024)
4-153586341-T-C		not specified	Uncertain significance (Feb 15, 2023)
4-153587783-G-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMEM131L	protein_coding	protein_coding	ENST00000409959	35	170366

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0403	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.693	798	855	0.933	0.0000445	10631
Missense in Polyphen		214	288.89	0.74077		3729
Synonymous	-0.596	334	320	1.04	0.0000186	3008
Loss of Function	6.67	16	80.6	0.199	0.00000379	1014

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000219	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000116	0.000105
Middle Eastern	0.000219	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Membrane-associated form that antagonizes canonical Wnt signaling by triggering lysosome-dependent degradation of Wnt-activated LRP6. Regulates thymocyte proliferation. {ECO:0000269|PubMed:23690469}.

Recessive Scores

• pRec: 0.0892

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.423
• hipred: N
• hipred_score: 0.384
• ghis: 0.503

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Tmem131l

Gene ontology

• Biological process: Wnt signaling pathway;negative regulation of immature T cell proliferation in thymus;negative regulation of canonical Wnt signaling pathway
• Cellular component: cytoplasm;endoplasmic reticulum;plasma membrane;integral component of membrane