Is CDAN1 p.Ser7Trp (c.20C>G) pathogenic?

CDAN1 p.Ser7Trp (c.20C>G) is classified Uncertain significance in CDAN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-11). AlphaMissense: likely benign (0.2356); Very rare (popmax 0.00122%, sas); Associated with Inborn genetic diseases.

What condition is associated with CDAN1 p.Ser7Trp (c.20C>G)?

CDAN1 p.Ser7Trp (c.20C>G) is associated with Inborn genetic diseases (ClinVar).

How common is CDAN1 p.Ser7Trp (c.20C>G) in the general population?

CDAN1 p.Ser7Trp (c.20C>G) is very rare (popmax 0.00122%, sas) (gnomAD).

What do computational predictors say about CDAN1 p.Ser7Trp (c.20C>G)?

AlphaMissense predicts likely benign (score 0.2356) — an in-silico prediction, not a clinical call.

CDAN1 p.Ser7Trp

c.20C>G · VCV3829691

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2356 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00122%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2356	likely benign
REVEL	0.457	indeterminate
SaProt	LLR -10.37	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.5	GERP 1.6, phastCons 1
Regional constraint	o/e 1.15	unconstrained · MANE · 1,562 bp · p 0.0016 · regional, not allelic
Overall
CADD	25.1	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 0.00122% South Asian · 1/81,962 alleles

Filtering AF 2.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000197% 3/1,526,260 alleles · very rare exomes 3/1,374,306 · genomes 0/151,954 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00122%	81,962
European (non-Finnish)	0.000176%	567,588

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: CDAN1
Protein: p.Ser7Trp
Coding: c.20C>G
MANE Select: NM_138477
Type: single nucleotide variant
Location: chr15:42737083 (GRCh38)
Gene constraint: LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 72.58 · 2 PDB
Residue 7: an α-helix

Full CDAN1 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

CDAN1 p.Ala1110Gly Uncertain significance ★★ ⚠ same condition
CDAN1 p.Ala887Glu Uncertain significance ★★ ⚠ same condition
CDAN1 p.Ala973Ser Uncertain significance ★★ ⚠ same condition
CDAN1 p.Arg1010Gln Uncertain significance ★★ ⚠ same condition
CDAN1 p.Arg282Gln Uncertain significance ★★ ⚠ same condition
CDAN1 p.Arg688Gln Uncertain significance ★★ ⚠ same condition
CDAN1 p.Arg864Trp Uncertain significance ★★ ⚠ same condition
CDAN1 p.Gln904His 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/cdan1-p-ser7trp (accessed [today's date]).

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