Is RMND1 p.Pro162fs (c.485del) pathogenic?

RMND1 p.Pro162fs (c.485del) is classified Pathogenic/Likely pathogenic in RMND1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-05). Very rare (popmax 0.000509%, nfe); Associated with RMND1-related disorder.

What condition is associated with RMND1 p.Pro162fs (c.485del)?

RMND1 p.Pro162fs (c.485del) is associated with RMND1-related disorder, combined oxidative phosphorylation defect type 11 (ClinVar).

How common is RMND1 p.Pro162fs (c.485del) in the general population?

RMND1 p.Pro162fs (c.485del) is very rare (popmax 0.000509%, nfe) (gnomAD).

RMND1 p.Pro162fs

c.485del · rs759477396 · VCV280833

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000509%, nfe)

Conditions

RMND1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -9.5	GERP -4.2
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000509% European (non-Finnish) · 6/1,178,824 alleles

Filtering AF 0.000183% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00012%

Overall 0.000372% 6/1,611,146 alleles · very rare exomes 6/1,458,814 · genomes 0/152,332 · 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.Pro162fs
Coding: c.485del
MANE Select: NM_017909
dbSNP: rs759477396
Type: Deletion
Location: chr6:151445327 (GRCh38)
Gene constraint: LOEUF 0.851 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 70.28

Full RMND1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

RMND1-related disorder

Also linked: combined oxidative phosphorylation defect type 11

Similar variants

RMND1 p.Leu412fs Pathogenic/Likely pathogenic ★★ same condition
RMND1 p.Lys405fs Pathogenic/Likely pathogenic ★★ same condition
RMND1 p.Thr97_Met98insTer Likely pathogenic ★★ same condition
RMND1 p.Val211fs Likely pathogenic ★★ same condition
RMND1 c.831-2_831-1del Likely pathogenic ★ same condition
RMND1 p.Glu286fs Pathogenic ★ same condition
RMND1 p.Phe36fs Pathogenic ★ same condition
RMND1 p.Thr243fs Likely pathogenic ★ same condition

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-pro162fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown