Is GEN1 p.Val148= (c.444C>T) pathogenic?

GEN1 p.Val148= (c.444C>T) is classified Likely benign in GEN1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-02). Very rare (popmax 0.008%, afr).

How common is GEN1 p.Val148= (c.444C>T) in the general population?

GEN1 p.Val148= (c.444C>T) is very rare (popmax 0.008%, afr) (gnomAD).

GEN1 p.Val148=

c.444C>T · rs542006404 · VCV2885919

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.008%, afr)

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 -0.52	GERP -4.5, phastCons 0.002
Overall
CADD	0.465	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.008% African / African-American · 6/75,038 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00228%

Overall 0.000805% 13/1,614,122 alleles · very rare exomes 5/1,461,824 · genomes 8/152,298 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.008%	12,506
Admixed American	0.00333%	30,009
East Asian	0.00223%	44,882
Remaining individualsnot grpmax-eligible	0.0016%	62,506
European (non-Finnish)	0.000254%	393,331

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: GEN1
Protein: p.Val148=
Coding: c.444C>T
MANE Select: NM_001130009
dbSNP: rs542006404
Type: single nucleotide variant
Location: chr2:17764992 (GRCh38)
Gene constraint: LOEUF 1.422 · pLI <0.01 · ClinGen HI dosage-sensitivity unlikely (gnomAD)
Structure: AlphaFold pLDDT 61.79 · 1 PDB
Residue 148: the 'xpg-i domain' region

Full GEN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GEN1 p.Val148Ala Uncertain significance ★ ⚠ same residue
GEN1 p.Val148Phe Uncertain significance ★ ⚠ same residue
GEN1 c.1264+1G>T Uncertain significance ★★ same type
GEN1 c.953+4A>G Uncertain significance ★★ same type
GEN1 p.Ala135Ser Uncertain significance ★★ ⚠ same type
GEN1 p.Ala197Thr Uncertain significance ★★ ⚠ same type
GEN1 p.Ala320Pro Uncertain significance ★★ ⚠ same type
GEN1 p.Ala447Val 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/gen1-p-val148 (accessed [today's date]).

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