TMEM201

Chr 1

transmembrane protein 201

Also known as: Ima1, NET5, SAMP1

NCBI Gene: 199953 ENSG00000188807 UniProt: Q5SNT2

Predicted to enable actin filament binding activity and lamin binding activity. Involved in several processes, including centrosome localization; positive regulation of endothelial cell migration; and protein localization to nuclear envelope. Located in cortical endoplasmic reticulum; nuclear inner membrane; and spindle pole centrosome. [provided by Alliance of Genome Resources, Jul 2025]

Research

ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.29

Clinical Summary— TMEM201

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

102 VUS of 132 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.29LOEUF

pLI 0.990

Z-score 4.29

OE 0.11 (0.05–0.29)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.33Z-score

OE missense 0.82 (0.75–0.90)

350 obs / 427.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.11 (0.05–0.29)

0≤0.351.4

Missense OE?0.82 (0.75–0.90)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 3 / 27.1Missense obs/exp: 350 / 427.2Syn Z: 0.32

This gene — mechanism propensity

0.4289th %ile

GOF

0.3689th %ile

LOF

0.74top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.29

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

132 submitted variants in ClinVar

ClinVar

Classification Summary

VUS102

Likely Benign8

Benign8

102

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	1	101	0	0	102
Likely Benign	0	7	0	1	8
Benign	0	3	1	4	8
Total	1	111	1	5	118

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

36 pathogenic / likely-pathogenic (of 46) ClinVar copy-number / structural variants overlap TMEM201 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →