RBM10

Chr X

RNA binding motif protein 10

Also known as: DXS8237E, GPATC9, GPATCH9, MINAS-60, S1-1, TARPS, ZRANB5

NCBI Gene: 8241 ENSG00000182872 UniProt: P98175

This protein binds to specific RNA sequences and regulates mRNA splicing, playing a critical role in post-transcriptional gene expression control. Mutations cause TARP syndrome, an X-linked recessive disorder affecting multiple organ systems. The gene is extremely intolerant to loss-of-function variants (pLI ~1.0, LOEUF 0.11), indicating that complete loss of protein function is typically incompatible with normal development.

ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a nuclear protein that belongs to a family proteins that contain an RNA-binding motif. The encoded protein associates with hnRNP proteins and may be involved in regulating alternative splicing. Defects in this gene are the cause of the X-linked recessive disorder, TARP syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2011]

ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.11

Clinical Summary— RBM10

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Gene-Disease Validity (ClinGen)

TARP syndrome · XLDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

31 unique Pathogenic / Likely Pathogenic· 149 VUS of 442 total submissions

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

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.11LOEUF

pLI 1.000

Z-score 5.94

OE 0.02 (0.01–0.11)

Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?

4.46Z-score

OE missense 0.40 (0.35–0.45)

172 obs / 433.4 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.02 (0.01–0.11)

0≤0.351.4

Missense OE?0.40 (0.35–0.45)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 1 / 43.1Missense obs/exp: 172 / 433.4Syn Z: 0.24

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

strongRBM10-related TARP syndromeLOFXLR

This gene — mechanism propensity

0.2499th %ile

GOF

0.2995th %ile

LOF

0.83top 5%

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

LOFprediction above median · 84% of P/LP variants are LoF · LOEUF 0.11

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

442 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14

Likely Pathogenic17

VUS149

Likely Benign116

Benign53

Conflicting9

Pathogenic

Likely Pathogenic

149

VUS

116

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	14	0	0	0	14
Likely Pathogenic	12	4	1	0	17
VUS	1	133	11	4	149
Likely Benign	0	14	40	62	116
Benign	0	7	23	23	53
Conflicting	—				9
Total	27	158	75	89	358

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

View in ClinVar →

65 pathogenic / likely-pathogenic (of 75) ClinVar copy-number / structural variants overlap RBM10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →