Is OMD p.Ser201Phe (c.602C>T) pathogenic?

OMD p.Ser201Phe (c.602C>T) is classified Uncertain significance in OMD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-07). AlphaMissense: likely benign (0.1351); Ultra-rare (popmax 0.0164%, mid).

How common is OMD p.Ser201Phe (c.602C>T) in the general population?

OMD p.Ser201Phe (c.602C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about OMD p.Ser201Phe (c.602C>T)?

AlphaMissense predicts likely benign (score 0.1351) — an in-silico prediction, not a clinical call.

OMD p.Ser201Phe

c.602C>T · rs776124805 · VCV2558778

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1351 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1351	likely benign
REVEL	0.15	moderately benign-leaning
SaProt	LLR -8.82	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.3, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 2,403 bp · p 0.054 · regional, not allelic
Overall
CADD	24.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,082 alleles

Filtering AF 0.0021% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.000496% 8/1,613,770 alleles · ultra-rare exomes 7/1,461,658 · genomes 1/152,112 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,082
South Asian	0.00549%	18,213
Admixed American	0.00167%	59,982
Remaining individualsnot grpmax-eligible	0.0016%	62,472

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: OMD
Protein: p.Ser201Phe
Coding: c.602C>T
MANE Select: NM_005014
dbSNP: rs776124805
Type: single nucleotide variant
Location: chr9:92416957 (GRCh38)
Gene constraint: LOEUF 0.757 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 81.82 · 1 PDB
Residue 201: an α-helix

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

Similar variants

OMD p.Arg336His Uncertain significance ★ same type
OMD p.Arg366Gln Uncertain significance ★ ⚠ same type
OMD p.Arg81Cys Uncertain significance ★ ⚠ same type
OMD p.Asn101Ser Uncertain significance ★ ⚠ same type
OMD p.Asn172Ser Uncertain significance ★ same type
OMD p.Asn187Asp Uncertain significance ★ ⚠ same type
OMD p.Asn369Thr Uncertain significance ★ ⚠ same type
OMD p.Asp30Asn Uncertain significance ★ ⚠ 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/omd-p-ser201phe (accessed [today's date]).

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