Is OMP p.Arg35Cys (c.103C>T) pathogenic?

OMP p.Arg35Cys (c.103C>T) is classified Uncertain significance in OMP (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-01). AlphaMissense: likely benign (0.2175); Ultra-rare (popmax 0.036%, afr).

How common is OMP p.Arg35Cys (c.103C>T) in the general population?

OMP p.Arg35Cys (c.103C>T) is ultra-rare (popmax 0.036%, afr) (gnomAD).

What do computational predictors say about OMP p.Arg35Cys (c.103C>T)?

AlphaMissense predicts likely benign (score 0.2175) — an in-silico prediction, not a clinical call.

OMP p.Arg35Cys

c.103C>T · rs781798033 · VCV3204306

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2175 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.036%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2175	likely benign
REVEL	0.22	benign-leaning
SaProt	LLR -12.35	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.9	GERP 1.8, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 488 bp · p 0.42 · regional, not allelic
Overall
CADD	26.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.036% African / African-American · 27/74,946 alleles

Filtering AF 0.0254% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0219%

Overall 0.0031% 50/1,612,964 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.036%	2,776
Middle Eastern	0.0329%	3,041
Admixed American	0.005%	20,004
Remaining individualsnot grpmax-eligible	0.0048%	20,820
East Asian	0.00223%	44,894
South Asian	0.0022%	45,546
European (non-Finnish)	0.00102%	98,325

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: OMP
Protein: p.Arg35Cys
Coding: c.103C>T
MANE Select: NM_004055 · reported on NM_006189
dbSNP: rs781798033
Type: single nucleotide variant
Location: chr11:77102942 (GRCh38)

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

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/omp-p-arg35cys (accessed [today's date]).

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