Is ERCC6L2 p.Ala26Val (c.77C>T) pathogenic?

ERCC6L2 p.Ala26Val (c.77C>T) is classified Uncertain significance in ERCC6L2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-12-06). Very rare (popmax 0.00168%, amr); Associated with Inborn genetic diseases.

What condition is associated with ERCC6L2 p.Ala26Val (c.77C>T)?

ERCC6L2 p.Ala26Val (c.77C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ERCC6L2 p.Ala26Val (c.77C>T) in the general population?

ERCC6L2 p.Ala26Val (c.77C>T) is very rare (popmax 0.00168%, amr) (gnomAD).

ERCC6L2 p.Ala26Val

c.77C>T · rs1317606477 · VCV1506440

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00168%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.19	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.21	GERP -0.69, phastCons 0.01
Regional constraint	o/e 1.16	unconstrained · MANE · 5,118 bp · p 0.073 · regional, not allelic
Overall
CADD	12.65	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00168% Admixed American · 1/59,690 alleles

Overall 0.000186% 3/1,612,128 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00168%	59,690
Remaining individualsnot grpmax-eligible	0.0016%	62,382
European (non-Finnish)	8.48e-05%	1,179,128

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: ERCC6L2
Protein: p.Ala26Val
Coding: c.77C>T
MANE Select: NM_020207
dbSNP: rs1317606477
Type: single nucleotide variant
Location: chr9:95880899 (GRCh38)
Gene constraint: LOEUF 0.792 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 58.11 · 2 PDB
Residue 26: the 'disordered' region

Full ERCC6L2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ERCC6L2 p.Ala26Ser Uncertain significance ★ same residue
ERCC6L2 p.Ala26= Likely benign ★ same residue
ERCC6L2 p.Ala290Val Uncertain significance ★★ same condition
ERCC6L2 p.Ala345Thr Uncertain significance ★★ same condition
ERCC6L2 p.Ala37Thr Uncertain significance ★★ same condition
ERCC6L2 p.Ala460Thr Uncertain significance ★★ same condition
ERCC6L2 p.Ala464Val Uncertain significance ★★ same condition
ERCC6L2 p.Ala465Gly 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/ercc6l2-p-ala26val (accessed [today's date]).

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