Is RMND1 p.Phe36fs (c.108del) pathogenic?

RMND1 p.Phe36fs (c.108del) is classified Pathogenic in RMND1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-23). Very rare (popmax 0.0011%, sas); Associated with combined oxidative phosphorylation defect type 11.

What condition is associated with RMND1 p.Phe36fs (c.108del)?

RMND1 p.Phe36fs (c.108del) is associated with combined oxidative phosphorylation defect type 11 (ClinVar).

How common is RMND1 p.Phe36fs (c.108del) in the general population?

RMND1 p.Phe36fs (c.108del) is very rare (popmax 0.0011%, sas) (gnomAD).

RMND1 p.Phe36fs

Q: How is Combined oxidative phosphorylation defect type 11 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.108del · rs767876357 · VCV2498152

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

combined oxidative phosphorylation defect type 11

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 1.7	GERP 2.1, phastCons 0.002
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 0.0011% South Asian · 1/91,072 alleles

Filtering AF 0.000542% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000428%

Overall 0.000805% 13/1,614,128 alleles · very rare exomes 13/1,461,852 · genomes 0/152,276 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,072
European (non-Finnish)	0.00102%	98,336

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.Phe36fs
Coding: c.108del
MANE Select: NM_017909
dbSNP: rs767876357
Type: Deletion
Location: chr6:151445704 (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

combined oxidative phosphorylation defect type 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Combined oxidative phosphorylation defect type 11 (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

RMND1 p.Leu412fs Pathogenic/Likely pathogenic ★★ same condition
RMND1 p.Lys405fs Pathogenic/Likely pathogenic ★★ same condition
RMND1 p.Pro162fs 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.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-phe36fs (accessed [today's date]).

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