RMND1 p.Arg424=
c.1270A>C · rs747587616 · VCV2414239
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00739%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.041 | GERP -4, phastCons 0.23 |
| Overall | ||
| CADD | 6.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00739%
European (non-Finnish) · 87/1,177,284 alleles
Filtering AF
0.00606%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00566%
Overall
0.00602%
97/1,610,914 alleles · very rare
exomes 92/1,458,724 · genomes 5/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00739% | 13,532 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,598 |
| Finnishnot grpmax-eligible | 0.00469% | 21,315 |
| African / African-American | 0.00267% | 37,434 |
| Admixed American | 0.00167% | 59,980 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RMND1
- Protein
- p.Arg424=
- Coding
- c.1270A>C
- MANE Select
- NM_017909
- dbSNP
- rs747587616
- Type
- single nucleotide variant
- Location
- chr6:151405767 (GRCh38)
- Gene constraint
- LOEUF 0.851 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 70.28
Similar variants
- RMND1 c.504+1G>A Pathogenic/Likely pathogenic ★★ same type
- RMND1 p.Arg23Ter Pathogenic/Likely pathogenic ★★ same type
- RMND1 p.Arg417Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- RMND1 p.Asn238Ser Pathogenic ★★ same type
- RMND1 p.Asp205Tyr Likely pathogenic ★★ ⚠ same type
- RMND1 p.Ter450Arg Pathogenic/Likely pathogenic ★★ same type
- RMND1 p.Ter450Ser Pathogenic/Likely pathogenic ★★ same type
- RMND1 p.Tyr196Ter Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rmnd1-p-arg424 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown