Is ELP5 p.Ser202Phe (c.605C>T) pathogenic?

ELP5 p.Ser202Phe (c.605C>T) is classified Uncertain significance in ELP5 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-14). AlphaMissense: likely benign (0.1834); Ultra-rare (popmax 0.0107%, afr).

How common is ELP5 p.Ser202Phe (c.605C>T) in the general population?

ELP5 p.Ser202Phe (c.605C>T) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

What do computational predictors say about ELP5 p.Ser202Phe (c.605C>T)?

AlphaMissense predicts likely benign (score 0.1834) — an in-silico prediction, not a clinical call.

ELP5 p.Ser202Phe

c.605C>T · rs769997557 · VCV2266965

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1834 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.1834	likely benign
REVEL	0.269	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.1	GERP 0.79, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 7,131 bp · p 0.95 · regional, not allelic
Overall
CADD	24.9	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.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S218F vs ClinVar S202F) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,918 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.000496% 8/1,614,054 alleles · ultra-rare

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: ELP5
Protein: p.Ser202Phe
Coding: c.605C>T
MANE Select: NM_203414
dbSNP: rs769997557
Type: single nucleotide variant
Location: chr17:7258601 (GRCh38)
Gene constraint: LOEUF 1.329 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.14

Full ELP5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ELP5 c.-17C>T Uncertain significance ★★ ⚠ same type
ELP5 p.Gly214Glu Benign ★★ same type
ELP5 c.-11G>T Uncertain significance ★ ⚠ same type
ELP5 c.-30G>T Uncertain significance ★ ⚠ same type
ELP5 p.Arg116Cys Uncertain significance ★ ⚠ same type
ELP5 p.Arg15Gly Uncertain significance ★ same type
ELP5 p.Arg188Gln Uncertain significance ★ ⚠ same type
ELP5 p.Arg193Cys 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/elp5-p-ser202phe (accessed [today's date]).

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