MR1

Chr 1

major histocompatibility complex, class I-related

Also known as: HLALS

NCBI Gene: 3140 ENSG00000153029 UniProt: Q95460

MAIT (mucosal-associated invariant T-cells) lymphocytes represent a small population of T-cells primarily found in the gut. The protein encoded by this gene is an antigen-presenting molecule that presents metabolites of microbial vitamin B to MAITs. This presentation may activate the MAITs to regulate the amounts of specific types of bacteria in the gut. Several transcript variants encoding different isoforms have been found for this gene, and a pseudogene of it has been detected about 36 kbp upstream on the same chromosome. [provided by RefSeq, Jul 2015]

Research

ResearchGenerating clinical summary…

DNmechanismLOEUF 1.83

Clinical Summary— MR1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

54 VUS of 72 total submissions

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Clinical Trials

2 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.83LOEUF

pLI 0.000

Z-score -1.33

OE 1.35 (0.97–1.83)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.34Z-score

OE missense 1.07 (0.95–1.20)

205 obs / 191.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.35 (0.97–1.83)

0≤0.351.4

Missense OE?1.07 (0.95–1.20)

0≤0.61.4

Synonymous OE?1.02

0≤1.21.6

LoF obs/exp: 23 / 17.1Missense obs/exp: 205 / 191.6Syn Z: -0.12

This gene — mechanism propensity

0.6551th %ile

GOF

0.5563th %ile

LOF

0.2969th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

72 submitted variants in ClinVar

ClinVar

Classification Summary

VUS54

Likely Benign4

Benign3

Conflicting1

VUS

Likely Benign

Benign

Conflicting

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	0	53	0	1	54
Likely Benign	0	4	0	0	4
Benign	0	1	0	2	3
Conflicting	—				1
Total	0	58	0	3	62

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

View in ClinVar →

28 pathogenic / likely-pathogenic (of 36) ClinVar copy-number / structural variants overlap MR1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →