RBMY1A1

Chr Y

RNA binding motif protein Y-linked family 1 member A1

Also known as: RBM, RBM1, RBM2, RBMY, RBMY1C, YRRM1, YRRM2

NCBI Gene: 5940ENSG00000234414UniProt: P0DJD3OMIM: 400006

The protein is an RNA-binding protein that regulates pre-mRNA splicing and is required for sperm development. Mutations cause male infertility due to azoospermia or severe oligospermia, with inheritance following a Y-linked pattern since the gene is located on the Y chromosome. The gene shows relatively low constraint to loss-of-function variants (pLI 0.29, LOEUF 1.89), consistent with its specialized role in male reproductive function.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.89
Clinical Summary— RBMY1A1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.89LOEUF
pLI 0.290
Z-score 0.28
OE 0.00 (0.00–1.89)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.34Z-score
OE missense 0.00 (0.00–1.75)
0 obs / 0.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–1.89)
0≤0.351.4
Missense OE0.00 (0.00–1.75)
0≤0.61.4
Synonymous OE0.00
0≤1.21.6
LoF obs/exp: 0 / 0.1Missense obs/exp: 0 / 0.9Syn Z: 0.43
DN
0.78top 25%
GOF
0.4776th %ile
LOF
0.3744th %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

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

RBMY1A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients