Is CSMD1 p.Ser1533= (c.4599C>T) pathogenic?

CSMD1 p.Ser1533= (c.4599C>T) is classified Likely benign in CSMD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-10). Very rare (popmax 0.00747%, nfe).

How common is CSMD1 p.Ser1533= (c.4599C>T) in the general population?

CSMD1 p.Ser1533= (c.4599C>T) is very rare (popmax 0.00747%, nfe) (gnomAD).

CSMD1 p.Ser1533=

c.4599C>T · VCV3497684

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00747%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.369	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.77	GERP -5.2
Overall
CADD	2.205	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00747% European (non-Finnish) · 87/1,164,976 alleles

Filtering AF 0.00613% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00572%

Overall 0.00599% 95/1,585,522 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00747%	13,391
Remaining individualsnot grpmax-eligible	0.00488%	20,473
African / African-American	0.00403%	24,807
Ashkenazi Jewishnot grpmax-eligible	0.00344%	29,056
Admixed American	0.00178%	56,212

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: CSMD1
Protein: p.Ser1533=
Coding: c.4599C>T
MANE Select: NM_033225
Type: single nucleotide variant
Location: chr8:3219328 (GRCh38)
Gene constraint: LOEUF 0.586 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Residue 1533: the cub 9 domain

Full CSMD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CSMD1 p.Ala1296Val Uncertain significance ★★ ⚠ same type
CSMD1 p.Asp908Ala Uncertain significance ★★ ⚠ same type
CSMD1 p.Asp927Asn Uncertain significance ★★ ⚠ same type
CSMD1 p.Gln308Leu Uncertain significance ★★ ⚠ same type
CSMD1 p.Glu1276Asp Uncertain significance ★★ ⚠ same type
CSMD1 p.Gly3156Arg Uncertain significance ★★ ⚠ same type
CSMD1 p.Ile1833Thr Uncertain significance ★★ ⚠ same type
CSMD1 p.Lys1718Asn 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/csmd1-p-ser1533 (accessed [today's date]).

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