Is ALB p.Ala239Ser (c.715G>T) pathogenic?

ALB p.Ala239Ser (c.715G>T) is classified Likely benign in ALB (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-08). AlphaMissense: likely benign (0.0907); Very rare (popmax 0.00401%, afr); Associated with Inborn genetic diseases.

What condition is associated with ALB p.Ala239Ser (c.715G>T)?

ALB p.Ala239Ser (c.715G>T) is associated with Inborn genetic diseases (ClinVar).

How common is ALB p.Ala239Ser (c.715G>T) in the general population?

ALB p.Ala239Ser (c.715G>T) is very rare (popmax 0.00401%, afr) (gnomAD).

What do computational predictors say about ALB p.Ala239Ser (c.715G>T)?

AlphaMissense predicts likely benign (score 0.0907) — an in-silico prediction, not a clinical call.

ALB p.Ala239Ser

c.715G>T · rs1339083689 · VCV2259168

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0907 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00401%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0907	likely benign
REVEL	0.109	moderately benign-leaning
SaProt	LLR -6.50	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.43	acceptor loss, 4 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -7.2	GERP -3.7
Overall
CADD	0.111	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00401% African / African-American · 3/74,874 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000496% 8/1,613,920 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00401%	24,958
European (non-Finnish)	0.000424%	236,001

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: ALB
Protein: p.Ala239Ser
Coding: c.715G>T
MANE Select: NM_001319193 · reported on NM_000477
dbSNP: rs1339083689
Type: single nucleotide variant
Location: chr4:73411997 (GRCh38)
Structure: AlphaFold pLDDT 64.11
Residue 239: the 'disordered' region

Full ALB 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

ALB p.Ala324Pro Uncertain significance ★★ ⚠ same condition
ALB p.Ala387Ser Uncertain significance ★★ ⚠ same condition
ALB p.Asp197Tyr Uncertain significance ★★ ⚠ same condition
ALB p.His27Pro Uncertain significance ★★ ⚠ same condition
ALB p.Thr590Ile Uncertain significance ★★ ⚠ same condition
ALB p.Ala150Ser Uncertain significance ★ ⚠ same condition
ALB p.Ala195Thr Uncertain significance ★ ⚠ same condition
ALB p.Ala200Val 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/alb-p-ala239ser (accessed [today's date]).

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