Is ERMN p.Pro83Ser (c.247C>T) pathogenic?

ERMN p.Pro83Ser (c.247C>T) is classified Likely benign in ERMN (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-21). AlphaMissense: likely benign (0.1197); Absent from gnomAD v4.1.

How common is ERMN p.Pro83Ser (c.247C>T) in the general population?

ERMN p.Pro83Ser (c.247C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ERMN p.Pro83Ser (c.247C>T)?

AlphaMissense predicts likely benign (score 0.1197) — an in-silico prediction, not a clinical call.

ERMN p.Pro83Ser

c.247C>T · rs769515247 · VCV2233992

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1197 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,599,666)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1197	likely benign
REVEL	0.055	moderately benign-leaning
SaProt	LLR -0.60	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 1.3	GERP -1.2, phastCons 0.81
Regional constraint	o/e 1.05	unconstrained · MANE · 4,368 bp · p 0.37 · regional, not allelic
Overall
CADD	8.835	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

No allele count reported in gnomAD v4.1 (AN 1,599,666). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ERMN
Protein: p.Pro83Ser
Coding: c.247C>T
MANE Select: NM_020711
dbSNP: rs769515247
Type: single nucleotide variant
Location: chr2:157324757 (GRCh38)
Gene constraint: LOEUF 0.963 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 57.95

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

Similar variants

ERMN p.Ala52Thr Benign ★★ same type
ERMN c.-27T>G Uncertain significance ★ same type
ERMN p.Ala11Asp Uncertain significance ★ ⚠ same type
ERMN p.Ala93Pro Uncertain significance ★ ⚠ same type
ERMN p.Arg110Gly Uncertain significance ★ ⚠ same type
ERMN p.Arg128Gly Uncertain significance ★ ⚠ same type
ERMN p.Arg147Gly Uncertain significance ★ ⚠ same type
ERMN p.Arg163Leu 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/ermn-p-pro83ser (accessed [today's date]).

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