Is CARNS1 p.Ser3Phe (c.8C>T) pathogenic?

CARNS1 p.Ser3Phe (c.8C>T) is classified Uncertain significance in CARNS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-01). Absent from gnomAD v4.1.

How common is CARNS1 p.Ser3Phe (c.8C>T) in the general population?

CARNS1 p.Ser3Phe (c.8C>T) is absent from gnomAD v4.1 (gnomAD).

CARNS1 p.Ser3Phe

c.8C>T · VCV3263342

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,377,052)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.048	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP -0.5, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 1,473 bp · p 0.039 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,377,052). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CARNS1
Protein: p.Ser3Phe
Coding: c.8C>T
MANE Select: NM_001166222
Type: single nucleotide variant
Location: chr11:67417411 (GRCh38)
Gene constraint: LOEUF 1.384 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.10

Full CARNS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CARNS1 p.Ala145Val Uncertain significance ★ ⚠ same type
CARNS1 p.Ala152Ser Uncertain significance ★ ⚠ same type
CARNS1 p.Ala190Thr Uncertain significance ★ ⚠ same type
CARNS1 p.Ala409Val Uncertain significance ★ ⚠ same type
CARNS1 p.Ala510Val Uncertain significance ★ ⚠ same type
CARNS1 p.Ala536Val Uncertain significance ★ ⚠ same type
CARNS1 p.Ala57Val Uncertain significance ★ same type
CARNS1 p.Ala619Asp 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/carns1-p-ser3phe (accessed [today's date]).

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