Is CLRN1 p.Val159Ala (c.476T>C) pathogenic?

CLRN1 p.Val159Ala (c.476T>C) is classified Uncertain significance in CLRN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-16). AlphaMissense: ambiguous (0.4576); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CLRN1 p.Val159Ala (c.476T>C)?

CLRN1 p.Val159Ala (c.476T>C) is associated with Inborn genetic diseases (ClinVar).

How common is CLRN1 p.Val159Ala (c.476T>C) in the general population?

CLRN1 p.Val159Ala (c.476T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CLRN1 p.Val159Ala (c.476T>C)?

AlphaMissense predicts ambiguous (score 0.4576) — an in-silico prediction, not a clinical call.

CLRN1 p.Val159Ala

c.476T>C · rs2472761845 · VCV2485472

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4576 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4576	ambiguous
REVEL	0.814	moderately pathogenic-leaning
SaProt	LLR -3.70	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8	GERP 0.7, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 45 kb · p 0.044 · regional, not allelic
Overall
CADD	22.3	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CLRN1
Protein: p.Val159Ala
Coding: c.476T>C
MANE Select: NM_174878
dbSNP: rs2472761845
Type: single nucleotide variant
Location: chr3:150928159 (GRCh38)
Gene constraint: LOEUF 1.168 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.74

Full CLRN1 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

CLRN1 p.Ala117Thr Uncertain significance ★★ ⚠ same condition
CLRN1 p.Arg207Gln Uncertain significance ★★ ⚠ same condition
CLRN1 p.Arg82Gly Uncertain significance ★★ ⚠ same condition
CLRN1 p.Gly70Cys Uncertain significance ★★ ⚠ same condition
CLRN1 p.His132Arg Uncertain significance ★★ ⚠ same condition
CLRN1 p.Ile109Thr Uncertain significance ★★ ⚠ same condition
CLRN1 p.Lys167Arg Uncertain significance ★★ ⚠ same condition
CLRN1 p.Met231Ile 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/clrn1-p-val159ala (accessed [today's date]).

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