Is ELP4 p.Ala79= (c.237C>T) pathogenic?

ELP4 p.Ala79= (c.237C>T) is classified Likely benign in ELP4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-22). Ultra-rare (popmax 0.0659%, mid); Associated with ELP4-related disorder.

What condition is associated with ELP4 p.Ala79= (c.237C>T)?

ELP4 p.Ala79= (c.237C>T) is associated with ELP4-related disorder (ClinVar).

How common is ELP4 p.Ala79= (c.237C>T) in the general population?

ELP4 p.Ala79= (c.237C>T) is ultra-rare (popmax 0.0659%, mid) (gnomAD).

ELP4 p.Ala79=

c.237C>T · rs373853950 · VCV3039471

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0659%, mid)

Conditions

ELP4-related disorder

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 -4.2	GERP -3.6
Overall
CADD	8.269	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0659% Middle Eastern · 4/6,066 alleles

Filtering AF 0.0224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0135%

Overall 0.00161% 26/1,612,430 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0659%	1,517
European (non-Finnish)	0.0017%	58,972
Remaining individualsnot grpmax-eligible	0.0016%	62,390
African / African-American	0.00134%	74,828

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: ELP4
Protein: p.Ala79=
Coding: c.237C>T
MANE Select: NM_019040
dbSNP: rs373853950
Type: single nucleotide variant
Location: chr11:31520069 (GRCh38)
Gene constraint: LOEUF 1.377 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.49

Full ELP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ELP4-related disorder

Similar variants

PAX6 p.Arg222Trp Pathogenic/Likely pathogenic ★★ same condition
PAX6 p.Ter437Leu Pathogenic/Likely pathogenic ★★ same condition
PAX6 c.*357A>T Uncertain significance ★★ same condition
PAX6 c.*2901T>C Benign/Likely benign ★★ same condition
ELP4 p.Thr392= Uncertain significance ★ same condition
ELP4 p.Val215Ile Uncertain significance ★ ⚠ same condition
PAX6 c.*1053T>C Uncertain significance ★ same condition
PAX6 c.*1287A>T Uncertain significance ★ same condition

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/elp4-p-ala79 (accessed [today's date]).

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