Is CELF3 p.Ala67Thr (c.199G>A) pathogenic?

CELF3 p.Ala67Thr (c.199G>A) is classified Uncertain significance in CELF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-04). AlphaMissense: likely benign (0.2775); Very rare (popmax 0.00573%, nfe).

How common is CELF3 p.Ala67Thr (c.199G>A) in the general population?

CELF3 p.Ala67Thr (c.199G>A) is very rare (popmax 0.00573%, nfe) (gnomAD).

What do computational predictors say about CELF3 p.Ala67Thr (c.199G>A)?

AlphaMissense predicts likely benign (score 0.2775) — an in-silico prediction, not a clinical call.

CELF3 p.Ala67Thr

c.199G>A · VCV4651859

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2775 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00573%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2775	likely benign
REVEL	0.14	moderately benign-leaning
SaProt	LLR -12.32	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.4, phastCons 1
Regional constraint	o/e 0.59	unconstrained · MANE · 8,731 bp · p 6.5e-15 · regional, not allelic
Overall
CADD	27.3	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 0.00573% European (non-Finnish) · 66/1,151,556 alleles

Filtering AF 0.00462% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00422%

Overall 0.00462% 72/1,559,622 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00573%	17,448
South Asian	0.00355%	28,169
Remaining individualsnot grpmax-eligible	0.00331%	30,228
African / African-American	0.00136%	73,422

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: CELF3
Protein: p.Ala67Thr
Coding: c.199G>A
MANE Select: NM_007185
Type: single nucleotide variant
Location: chr1:151714623 (GRCh38)
Gene constraint: LOEUF 0.662 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.04 · 1 PDB
Residue 67: the rrm 1 domain

Full CELF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CELF3 p.Ala146Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala206Ser Uncertain significance ★ ⚠ same type
CELF3 p.Ala206Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala216Glu Uncertain significance ★ ⚠ same type
CELF3 p.Ala221Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala276Thr Uncertain significance ★ ⚠ same type
CELF3 p.Ala312Val Uncertain significance ★ ⚠ same type
CELF3 p.Ala323Thr 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/celf3-p-ala67thr (accessed [today's date]).

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