Is CELF1 p.Ser507= (c.1521G>A) pathogenic?

CELF1 p.Ser507= (c.1521G>A) is classified Benign in CELF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-04-06). Rare (popmax 0.977%, mid).

How common is CELF1 p.Ser507= (c.1521G>A) in the general population?

CELF1 p.Ser507= (c.1521G>A) is rare (popmax 0.977%, mid) (gnomAD).

CELF1 p.Ser507=

c.1521G>A · rs145495807 · VCV791545

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.977%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.48	GERP -2.1, phastCons 0.03
Overall
CADD	12.48	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.977% Middle Eastern · 59/6,038 alleles

Filtering AF 0.778% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.706%

Overall 0.211% 3,410/1,614,156 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.01%	99
Middle Easterngrpmax	0.977%	102
South Asian	0.292%	342
Remaining individualsnot grpmax-eligible	0.232%	431
European (non-Finnish)	0.211%	474
Finnishnot grpmax-eligible	0.0952%	1,050
Admixed American	0.0933%	1,072
African / African-American	0.036%	2,780
East Asian	0.0178%	5,610

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CELF1
Protein: p.Ser507=
Coding: c.1521G>A
MANE Select: NM_001376376
dbSNP: rs145495807
Type: single nucleotide variant
Location: chr11:47472254 (GRCh38)
Gene constraint: LOEUF 0.247 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.17 · 8 PDB

Full CELF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CELF1 c.606+2T>A Uncertain significance ★ same type
CELF1 p.Ala237Thr Uncertain significance ★ ⚠ same type
CELF1 p.Ala401Val Uncertain significance ★ same type
CELF1 p.Ala99Val Uncertain significance ★ ⚠ same type
CELF1 p.Arg152Gln Uncertain significance ★ same type
CELF1 p.Arg506His Uncertain significance ★ ⚠ same type
CELF1 p.Arg60Gln Uncertain significance ★ ⚠ same type
CELF1 p.Arg96His 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/celf1-p-ser507 (accessed [today's date]).

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