TMEM131L

protein-coding

transmembrane 131 like

Gene summary

Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of immature T cell proliferation in thymus. Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA0922

MANE transcript

NM_001131007.2

Inheritance

—

ClinVar variants

U:245B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr4:153,466,346-153,636,711

External References & Databases

Ensembl (ENSG00000121210)

Transcript & Mutation Effects

hg38 • Region Span ~170.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM131L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 249

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001131007.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar	1 clinvar	4
missense			240 clinvar	14 clinvar	1 clinvar	255
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	245	16	2	263

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 90 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001131007.2	RefSeq	NP_001124479.1	35	MANE Select
ENST00000409959.8	Ensembl	ENSP00000386787.3	35	MANE Select
NM_015196.4	RefSeq	NP_056011.3	35	Standard
ENST00000240487.5	Ensembl	ENSP00000240487.5	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409959
Coding exons: 35
Length: 170366
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125748
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.693	798	855	0.933	0.0000445	10631
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N