Is CCSAP p.Arg37Cys (c.109C>T) pathogenic?

CCSAP p.Arg37Cys (c.109C>T) is classified Uncertain significance in CCSAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-11). AlphaMissense: likely pathogenic (0.9698); Absent from gnomAD v4.1.

How common is CCSAP p.Arg37Cys (c.109C>T) in the general population?

CCSAP p.Arg37Cys (c.109C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCSAP p.Arg37Cys (c.109C>T)?

AlphaMissense predicts likely pathogenic (score 0.9698) — an in-silico prediction, not a clinical call.

CCSAP p.Arg37Cys

c.109C>T · rs1404524258 · VCV2475782

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9698 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,508,388)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9698	likely pathogenic · top 7% in CCSAP
REVEL	0.741	pathogenic-leaning
SaProt	LLR -9.74	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP -1.2, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 17 kb · p 0.13 · regional, not allelic
Overall
CADD	27.5	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

No allele count reported in gnomAD v4.1 (AN 1,508,388). 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: CCSAP
Protein: p.Arg37Cys
Coding: c.109C>T
MANE Select: NM_145257
dbSNP: rs1404524258
Type: single nucleotide variant
Location: chr1:229342357 (GRCh38)
Gene constraint: LOEUF 1.472 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.61

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

Similar variants

CCSAP p.Ala113Thr Uncertain significance ★ ⚠ same type
CCSAP p.Ala208Thr Uncertain significance ★ ⚠ same type
CCSAP p.Arg14His Uncertain significance ★ ⚠ same type
CCSAP p.Arg152Gln Uncertain significance ★ ⚠ same type
CCSAP p.Arg224Gly Uncertain significance ★ ⚠ same type
CCSAP p.Arg235Ser Uncertain significance ★ ⚠ same type
CCSAP p.Asp115Glu Uncertain significance ★ ⚠ same type
CCSAP p.Asp143Glu 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/ccsap-p-arg37cys (accessed [today's date]).

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