Is CELA1 p.Val3fs (c.7_8del) pathogenic?

CELA1 p.Val3fs (c.78del) is classified Benign in CELA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-04-25). Very rare (popmax 0.00242%, nfe).

How common is CELA1 p.Val3fs (c.7_8del) in the general population?

CELA1 p.Val3fs (c.7_8del) is very rare (popmax 0.00242%, nfe) (gnomAD).

CELA1 p.Val3fs

c.7_8del · rs1491233894 · VCV402531

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00242%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.9	GERP -3.6
Overall
CADD	19.52	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00242% European (non-Finnish) · 27/1,115,446 alleles

Filtering AF 0.00166% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00142%

Overall 0.00201% 30/1,491,864 alleles · very rare exomes 24/1,438,368 · genomes 6/53,496 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00242%	41,313
Admixed American	0.00211%	47,424
African / African-American	0.00202%	49,480
Remaining individualsnot grpmax-eligible	0.00166%	60,128

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: CELA1
Protein: p.Val3fs
Coding: c.7_8del
MANE Select: NM_001971
dbSNP: rs1491233894
Type: Deletion
Location: chr12:51346631 (GRCh38)
Gene constraint: LOEUF 1.267 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.54

Full CELA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/cela1-p-val3fs (accessed [today's date]).

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