Is LDLR p.Ser195= (c.585C>T) pathogenic?

LDLR p.Ser195= (c.585C>T) is classified Likely benign in LDLR (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-03-12). Rare (popmax 0.132%, mid); Associated with hypercholesterolemia, familial, 1.

What condition is associated with LDLR p.Ser195= (c.585C>T)?

LDLR p.Ser195= (c.585C>T) is associated with hypercholesterolemia, familial, 1, familial hypercholesterolemia (ClinVar).

How common is LDLR p.Ser195= (c.585C>T) in the general population?

LDLR p.Ser195= (c.585C>T) is rare (popmax 0.132%, mid) (gnomAD).

LDLR p.Ser195=

c.585C>T · rs756880555 · VCV921742

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.132%, mid)

Conditions

hypercholesterolemia, familial, 1

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 0.23	GERP -4.5, phastCons 0.021
Overall
CADD	1.927	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.132% Middle Eastern · 8/6,062 alleles

Filtering AF 0.0656% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0478%

Overall 0.000867% 14/1,614,020 alleles · rare exomes 13/1,461,674 · genomes 1/152,346 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.132%	758
Admixed American	0.00333%	30,010
Remaining individualsnot grpmax-eligible	0.0032%	31,255
European (non-Finnish)	0.000169%	590,023

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: LDLR
Protein: p.Ser195=
Coding: c.585C>T
MANE Select: NM_000527
dbSNP: rs756880555
Type: single nucleotide variant
Location: chr19:11105491 (GRCh38)
Gene constraint: LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.81 · 36 PDB
Residue 195: the 'binding to getah virus e1-e2 spike glycoproteins' region; the ldl-receptor class a 5 domain

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

Disease context

hypercholesterolemia, familial, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial hypercholesterolemia

Similar variants

LDLR p.Ser195Arg Uncertain significance ★ ⚠ same residue
LDLR p.Ser195Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
LDLR p.Ser195fs Pathogenic ★ same residue
LDLR c.1186+5G>A Likely pathogenic ★★★ same condition
LDLR c.1359-1G>A Pathogenic ★★★ same condition
LDLR c.1359-5C>G Likely pathogenic ★★★ same condition
LDLR c.1705+2T>C Likely pathogenic ★★★ same condition
LDLR c.190+4A>T Likely pathogenic ★★★ 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/ldlr-p-ser195 (accessed [today's date]).

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