RMND1 p.Phe101=
c.303T>C · rs1387358151 · VCV2974864
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.15 | GERP -4.2 |
| Overall | ||
| CADD | 3.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
African / African-American · 5/74,948 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00031%
5/1,614,132 alleles · very rare
exomes 3/1,461,888 · genomes 2/152,244 · joint denominator
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.Phe101=
- Coding
- c.303T>C
- MANE Select
- NM_017909
- dbSNP
- rs1387358151
- Type
- single nucleotide variant
- Location
- chr6:151445509 (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-phe101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown