Is CSH1 p.Ala39= (c.117T>C) pathogenic?

CSH1 p.Ala39= (c.117T>C) is classified Likely benign in CSH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-01). Absent from gnomAD v4.1.

How common is CSH1 p.Ala39= (c.117T>C) in the general population?

CSH1 p.Ala39= (c.117T>C) is absent from gnomAD v4.1 (gnomAD).

CSH1 p.Ala39=

c.117T>C · rs2509198674 · VCV2648083

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 732,600)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.5	GERP -3.7
Overall
CADD	0.683	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 732,600). 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: CSH1
Protein: p.Ala39=
Coding: c.117T>C
MANE Select: NM_001317
dbSNP: rs2509198674
Type: single nucleotide variant
Location: chr17:63896129 (GRCh38)
Gene constraint: LOEUF 1.213 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.67 · 1 PDB
Residue 39: an α-helix

Full CSH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSH1 p.Ala14Gly Uncertain significance ★ ⚠ same type
CSH1 p.Ala2Thr Uncertain significance ★ ⚠ same type
CSH1 p.Arg159His Uncertain significance ★ ⚠ same type
CSH1 p.Arg160Trp Uncertain significance ★ ⚠ same type
CSH1 p.Arg204Ser Uncertain significance ★ ⚠ same type
CSH1 p.Arg6Gln Uncertain significance ★ ⚠ same type
CSH1 p.Asp135Asn Uncertain significance ★ ⚠ same type
CSH1 p.Asp180His 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/csh1-p-ala39 (accessed [today's date]).

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